title: control diet, male, biol rep 1


title: Hypoxia_H3K9la_Input

status: Public on May 22 2024

type: SRA

city: tianjin

first: yong

last: zang

address: Heping District qixiangtailu22hao

country: China

institute: Tianjin Medical University

library_source: genomic

data_processing:
RNA-Seq
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through fastp software.
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . padj<=0.05 and |log2(foldchange)| >= 1 were set as the threshold for significantly differential expression.
ChIP-Seq
we used Fastp (version 0.19.7) to perform basic statistics on the quality of the raw reads.
Quality control was performed by FastQC software.
Clean reads were aligned to the human reference genome (hg 38) by bowtie 2 ChIP-seq peaks were detected by the peak-finding algorithm MACS2,the significance cut-off q-value <=0.05.
bigWig files were generated using the genomicRanges R package.
Assembly: hg38
Supplementary files format and content: xls files include FPKM values for each Sample
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Homo sapiens

source_name: oesophagus

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. MNase treated cells for 15 min at 37℃. The DNA were purified using glycogen.
10ng DNA was used as starting material for input and ip samples.After the DNA samples quality control，the purified DNA was used NEBNext® Ultra™ II DNA Library Prep Kit （NEB, USA, Catalog #: E7645L）for ChIP-seq library preparation.

tag: tissue

value: oesophagus

tag: cell line

tag: cell type

value: esophageal squamous cell carcinoma

tag: genotype

value: WT

tag: protocol

value: hypoxia


title: PLX5622 diet, replicate 1

city: La Jolla

first: Caterina

last: Profaci

address: 9500 Gilman Drive

country: USA

institute: University of California, San Diego

library_source: transcriptomic single cell

data_processing:
Gene counts were obtained by aligning reads to the mm10 genome (refdata-gex-mm10-2020-A) using CellRanger software (v.6.0.1 – 10X Genomics). Using Seurat (v.4.0), quality control was performed using the following: 1) outliers with a high ratio of mitochondrial RNAs (>5%, <200 features) relative to endogenous RNAs and homotypic doublets (>5000 features) were removed in Seurat; 2) after scTransform normalization and integration, doublets and multiplets were removed using DoubletFinder; 3) cells were manually inspected using known cell-type specific marker genes, cells expressing more than one cell-type specific marker were removed.
In Seurat (v.4.0), gene counts were first normalized using scTransform, then Integration function was used to align data with default settings. Genes were projected into principal component (PC) space using the principal component analysis function RunPCA. The first 30 dimensions were used as inputs into Seurat’s FindNeighbors and FindClusters functions. Then, RunUMAP function with default settings was used to calculate 2-dimensional UMAP coordinates and search for distinct cell populations.
Distinct cell types were determined using known cell-type specific markers. Differential gene expression of genes comparing PLX5622 to control samples was performed with the FindMarkers function, specifically utilizing the Wilcoxon Rank Sum test.
Assembly: mm39
Supplementary files format and content: barcodes, features, and matrix for each sample

molecule: total RNA

organism: Mus musculus

source_name: brain

extract_protocol:
Mice were anesthetized with ketamine/xylazine and decapitated. Brains were removed, meninges were peeled off, and cerebellum and olfactory bulbs were discarded.  A series of enzymatic and mechanical steps was used to achieve a single cell suspension of the remaining brain tissue. FACS was used to enrich for CD31+ endothelial cells, which were sorted for single-cell sequencing. Brains from three mice were used across the two samples.
Libraries were constructed with the 10X Genomics Chromium Next GEM Single Cell 3’ kit v3.1 according to manufacturer's instructions

treatment_protocol: Mice were kept on control or PLX5622 (1200 ppm) diet for one month

value: brain

value: sorted endothelial cells

tag: treatment

value: PLX5622 diet, 1200 ppm

tag: treatment duration

value: 1 month

tag: strain


title: Normoxia_H3K9la_Input

value: normoxia


title: Normoxia_H3K9la_IP

tag: antibody


title: PLVX_LAMC2_3xFlag_2_KYSE30

description:
LAMC2vsPLVX_deg.xls
PLVX_2

library_source: transcriptomic

extract_protocol:
RNA was harvested using Trizol.800ng of total RNA was used for the construction of sequencing libraries.
otal RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained. In order to ensure the quality of the library, the library needs to be tested. After the construction of the library, the library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by Agilent 2100 bioanalyzer. After insert size meets the expectation, qRT-PCR is used to accurately quantify the effective concentration of the library (the effective concentration of the library is higher than that of 2nM) to ensure the quality of the library.

value: LAMC2 overexpressed


title: Hypoxia_H3K9la_IP


title: PLX5622 diet, replicate 2


title: control diet, replicate 1

value: control diet


title: PLVX_LAMC2_3xFlag_3_KYSE30

description:
LAMC2vsPLVX_deg.xls
PLVX_3


title: control diet, replicate 2


title: PLVX_LAMC2_3xFlag_1_KYSE30

description:
LAMC2vsPLVX_deg.xls
PLVX_1


title: PLX5622 diet, astrocyte ribotag, biol rep 3

data_processing:
Raw paired-end sequencing data were aligned to the mouse genome (mm39 – UCSC Genome Browser) using STAR (v2.7.10a).
Gene counts were obtained using the featureCounts function from the R package Subread (v2.0.1).
Differential expression analysis was performed using default settings with DESeq2 (v1.32.0) in R (v4.1.0).
Assembly: mm39
Supplementary files format and content: excel file contains TPM values as well as DESeq2 statistics results

molecule: polyA RNA

extract_protocol:
Mice were were euthanized with carbon dioxide, and brains were homogenized and incubated with anti-HA antibody. Magnetic IgG beads were used to isolate ribosome-bound mRNA. RNA was purified using the RNeasy Micro kit from Qiagen.
Non-stranded mRNA libraries were made using Illumina's TruSeq RNA Library Prep Kit v2 according to manufacturer's instructions

treatment_protocol: Mice were kept on control or PLX5622 (1200 ppm) diet for one month.

value: astrocytes with some neurons and oligodendrocytes

value: Gfap-Cre; RiboTag


title: GFP1

city: WORCESTER

first: Susu

last: Guo

state: MA

address: 7 Pocono Road

institute: UMASS Chan Medical School

data_processing:
ATAC-seq bioinformatics data analysis was performed following Harvard FAS Informatics ATAC_x0002_seq Guidelines. Briefly, fastp software (v0.20.0) was used to trim adaptor and remove low quality reads to get high quality clean reads. Then these clean reads were aligned to human reference genome (hg38) using bowtie2 software (v2.2.4). ATACseqQC R package (v1.22.0) was used to calculate and plot the fragment size distribution. Deeptools software (v3.5.1) was used to calculate and plot the correlations. Genrich software (v1.30.3) was used for peak calling and blacklist regions were removed. ChIPseeker R package (v1.30.3) was used to annotate the enriched peaks. Homer software (v4.11) was used to identify motifs. MANorm2 R package was used to perform differentially enriched region analysis between two groups of samples. GO and KEGG Pathway enrichment analysis were performed with ClusterProfiler R package (v3.18.1) based on the enriched peak and differentially enriched region_x0002_associated genes. And the enriched peaks were visualized in IGV (v2.64) software.
Assembly: mm10
Supplementary files format and content: ATAC.xlsx

growth_protocol: DMEM with 10% FBS

extract_protocol:
Nuclear extraction kit (Solarbio) was used to prepare the library.
Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme) was used to prepare ATAC-seq library according to the protocol.

treatment_protocol: HEK293T cells were transient transfected with VGLL2-NCOA2, YAP5SA or GFP plasmids.

value: Human embryonic kidney cells

value: GFP

value: transient transfection GFP


title: PLX5622 diet, astrocyte ribotag, biol rep 2


title: PLVX_1_KYSE30

description:
LAMC2vsPLVX_deg.xls
LAMC2_1

value: Control


title: control diet, astrocyte ribotag, biol rep 2


title: PLX5622 diet, astrocyte ribotag, biol rep 1


title: Golden ringtail possum (Sample1771)

city: Houston

first: Olga

last: Dudchenko

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Short-read assembly using w2rap (Clavijo, 2017); Hi-C-guided genome assembly (Juicer, 3D-DNA, JBAT); RagTag assembler (Alonge et al., 2022) for Dactylopsila trivirgata and Distoechurus pennatus
Assembly: Generated as part of the study
Supplementary files format and content: fasta.gz: chromosome-length nucleotide sequences generated usign Hi-C-guided genome assembly; RagTag assisted assemblies for Dactylopsila trivirgata and Distoechurus pennatus
Library strategy: In situ Hi-C; ClaSeek PCR-free DNA-Seq.

organism: Pseudochirops corinnae

source_name: kidney

extract_protocol:
Extractions for WGS libraries were done using DNeasy blood & tissue kit
The Hi-C libraries were prepared following the in situ Hi-C strategy (Rao, Huntley et al., 2014). Briefly, cells or tissue were crosslinked and then lysed with nuclei permeabilized but still intact. DNA was then restricted and the overhangs filled in incorporating a biotinylated base. Free ends were then ligated together in situ. Crosslinks were reversed, the DNA was sheared to 300-500bp and then biotinylated ligation junctions were recovered with streptavidin beads. Afterward DNA was handled according to standard Illumina library construction protocol. DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo-) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3 end. After adapter ligation DNA was PCR amplified with Illumina primers and library fragments of 400-600 bp (insert plus adaptor and PCR primer sequences) were purified using SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on various Illumina instruments following the manufacturer's protocols. Fpr the tammar wallaby, a short insert-size PCR-free DNA-Seq library was prepared following the ClaSeek protocol.

value: kidney


title: PLVX_3_KYSE30

description:
LAMC2vsPLVX_deg.xls
LAMC2_3

value: oesophagus

value: esophageal squamous cell carcinoma


title: control diet, astrocyte ribotag, biol rep 1


title: PLVX_2_KYSE30

description:
LAMC2vsPLVX_deg.xls
LAMC2_2


title: Green ringtail possum (Sample1772)

organism: Pseudochirops archeri


title: control diet, astrocyte ribotag, biol rep 3


title: Feathertail glider (Sample1774)

organism: Acrobates pygmaeus

source_name: liver

value: liver


title: normoxia_3_KYSE30

description:
OvsH_deg.xls
O3

value: WT


title: normoxia_2_KYSE30

description:
OvsH_deg.xls
O2


title: YAP5SA1

value: transient transfection YAP5SA


title: thalamus,WT,thalamus_8

city: Edinburgh

first: Nadine

last: Bestard-Cuche

address: 5 Little France Drive

country: United Kingdom

institute: University of Edinburgh

description: 10x Genomics

data_processing:
The alignment to the reference genome, demultiplexing, barcoded processing, gene counting and cell calling were made using the Cell Ranger software (v5.0.0 to v7.00).
Cells were filtered based on output from isOutlier function from scater (v1.20.1), genes expressed in less than two cells were discarded, normalisation was performed by deconvulation ( with scran v1.20.1).
Selection of variable genes, dimensional reduction, batch correction when needed (with fastMNN from batchelor v1.8.0) and clustering (with scran) was performed a first time, then a clusterQC and a stricter QC was performed to retain only high quality cells, annotation was performed with marker genes. More details regarding the differences between datasets can be found in the paper.
Assembly: mm10
Supplementary files format and content: SingleCellExperiment_RDSs contains R files for each dataset. It is the fully cleaned, normalised, batch corrected and annotated version.
Supplementary files format and content: cellinfo_CSVs.tar contains the metadata for the cells from all the cleaned datasets. Each row is a cell and each column has infromation such as the qc parametres or the cell annotation
Supplementary files format and content: cellranger_matrices.tar has the filtered and raw matrices from cellranger output.

source_name: thalamus

extract_protocol:
Mice were culled via cervical dislocation and brains were dissected, with the olfactory bulbs and cerebellum being removed.The desired area of the brain were collected in ice-cold HBSS (w/o Ca2+ and Mg2+; 14175-053; Gibco) with 5% trehalose (T0167; Sigma Aldrich) and 30 µM actinomycin D (A1410; Sigma Aldrich) and were finely minced using a 22A scalpel. Brains were digested using the Adult Brain Dissociation Kit (130-107-677; Miltenyi Biotec), with the following modifications: (i) tissues were dissociated as described in the “manual dissociation” section of the Neural Tissue Dissociation Kit protocol (130-092-628; Miltenyi Biotec), (ii) enzymatic digestions were performed at 35°C, (iii) half the concentration of enzyme P was used, (iv) actinomycin D was used to limit dissociation-induced transcriptional changes,  (v) 5% trehalose was added in all buffers to increase cellular viability, (vi) cell clusters were removed by filtration through prewetted 70 μm (352350; Falcon) and 40 μm (352340; Falcon) cell strainers, (vii) erythrocyte and myelin debris removal steps were omitted during dissociation steps, and (viii) all centrifugations were performed at 200 g at 4°C. After dissociation, cells were collected in PBS with 0.2% BSA before being sorted on a Sony SH800 cell sorter. Gates were chosen based on forward and side scatter to exclude myelin debris, erythrocytes, and doublets. Non-viable cells were excluded based on Draq7 and/or DAPI staining (Draq7high and/or DAPIhigh cells were classified as non-viable).
single cells were processed through the Chromium Single Cell Platform using the Chromium Next GEM Single Cell 3’ GEM Library and Gel Bead Kit (v3.1 chemistry, PN-1000121, 10x genomics) and the Chromium Next GEM Chip G kit (PN-1000120) and processed following manufacturer’s instructions.

value: thalamus

tag: exit age

value: 1y 5m 7d

tag: Sex

value: M

tag: mouse


title: Common ringtail possum (Sample1769)

organism: Pseudocheirus peregrinus

source_name: muscle

value: muscle


title: PaleoHi-C of Mammuthus primigenius DNA Zoo Sample6310, PeloHi-C lib id: S_mm_eth_sup_505

description:
MamPri_Loxafr3.0_assisted.hic
MamPri_Loxafr3.0_assisted_HiC.toga_annotations.bed
MamPri_Loxafr3.0_assisted_HiC.fasta.gz
MamPri_Loxafr3.0_assisted.rawchrom.hic
MamPri_ASM1433276v1_assisted_HiC.fasta.gz
MamPri_ASM1433276v1_assisted.hic
MamPri_ASM1433276v1_assisted.rawchrom.hic
Loxafr3.0_mock_HiC.assembly
Loxafr3.0_mock_HiC.fasta.gz
MP_skin_CRUSH_Loxafr3.0_HiC.bedgraph
MP_MamPri_Loxafr3.0_assisted_HiC.hic
MP_MamPri_Loxafr3.0_assisted_HiC_30.hic
MP_MamPri_ASM1433276v1_assisted_HiC_30.hic
MP_MamPri_ASM1433276v1_assisted_HiC.hic
MP_EtOH_Loxafr3.0_HiC_30.hic
MP_EtOH_Loxafr3.0_HiC.hic
MP_Loxafr3.0_HiC_30.hic
MP_Loxafr3.0_HiC.hic
PaleoHi-C_extended_reference.hic
direct_inversion_chr10_Loxafr3.0_HiC.hic
MiChroM_Loxafr3.0_HiC.hic
Woolly_Mammoth_Direct_Inv.sw
Woolly_Mammoth_MiChroM.sw

data_processing:
Hi-C-guided genome assembly (3D-DNA, JBAT)
Reference-guided 3D genome assembly (Anonamos, 3D-DNA, JBAT)
Construction of the chromosome-length Hi-C contact map (BWA, Juicer, 3D-DNA)
liftover (KentUtils, 3D-DNA)
Gene annotation (TOGA)
Compartment annotation (CRUSH)
Loop calling and aggregate analysis (HiCCUPS, Juicer Tools, SIP, SIP META)
Aggregate chromosome analysis (3D-DNA)
Modeling of 3D structures of woolly mammoth chromosomes (OpenMiChroM)
DNA degradation simulations (NuChroM, custom script)
Assembly: The following existing genome builds were used in parts of the study: Loxafr3.0 (GCA_000001905.1), ASM1433276v1 (GCA_014332765.1), EquCab2.0 (GCF_000002305.2), ASM303372v1 (GCA_003033725.1), bosTau9 (GCF_002263795.3), ASM651725v1 (GCF_006517255.1), ASM3043605v1 (GCF_030436055.1), ASM331443v2 (GCF_003314435.2), hg38, hg19.
Supplementary files format and content: fasta.gz: chromosome-length nucleotide sequences generated usign Hi-C-guided genome assembly
Supplementary files format and content: hic: contact maps generated by aligning Hi-C data to reference sequences. In addition to "standard" hic maps build against chromosome-length references included are "assembly" maps generated by 3D-DNA for before and after genome assembly and an aggregate chromosome analysis (ACA) map.
Supplementary files format and content: bedpe: chromatin loops
Supplementary files format and content: bedgraph: A/B compartment annotations
Supplementary files format and content: sw: HDF5-based file for storing 3D structure ensembles
Supplementary files format and content: assembly: text file describing the relationship between the draft assembly and the chromosome-length upgrade
Supplementary files format and content: bed: gene annotations

organism: Mammuthus primigenius

source_name: skin

extract_protocol:
The protocol is described in detail in Sandoval-Velasco, Dudchenko, Rodríguez, Pérez Estrada et al., 2024. Briefly, PaleoHi-C is a a modified in situ Hi-C protocol, tailored towards working with highly degraded samples. The principal modifications were: (i) immediate preservation in the field using ethanol to reduce microbial activity; and (ii) sequestration of chromatin bodies on beads; (iii) removal of shearing and size selection given the lack of high molecular weight DNA; and (iv) library amplification using a paleo-compatible workflow
Library contruction protocol is described in detail in Sandoval-Velasco, Dudchenko, Rodríguez, Pérez Estrada et al., 2024.
Modified Hi-C.

value: skin

value: EtOH-preserved on site


title: thalamus,KO,thalamus_7

description: 10x Genomics

value: KO


title: PaleoHi-C of Mammuthus primigenius DNA Zoo Sample6310, PeloHi-C lib id: S_mm_eth_504


title: normoxia_1_KYSE30

description:
OvsH_deg.xls
O1

value: normoxia


title: thalamus,KO,thalamus_5

description: 10x Genomics

value: F


title: PaleoHi-C of Mammuthus primigenius DNA Zoo Sample6310, PeloHi-C lib id: A_mm_eth_sup_502


title: hypoxia_3_KYSE30

description:
OvsH_deg.xls
H3

value: hypoxia


title: thalamus,WT,thalamus_6

description: 10x Genomics


title: PaleoHi-C of Mammuthus primigenius DNA Zoo Sample6311, PeloHi-C lib id: 532

description:
MamPri_Loxafr3.0_assisted.hic
MamPri_Loxafr3.0_assisted_HiC.toga_annotations.bed
MamPri_Loxafr3.0_assisted_HiC.fasta.gz
MamPri_Loxafr3.0_assisted.rawchrom.hic
MamPri_ASM1433276v1_assisted_HiC.fasta.gz
MamPri_ASM1433276v1_assisted.hic
MamPri_ASM1433276v1_assisted.rawchrom.hic
Loxafr3.0_mock_HiC.assembly
Loxafr3.0_mock_HiC.fasta.gz
MP_skin_CRUSH_Loxafr3.0_HiC.bedgraph
MP_MamPri_Loxafr3.0_assisted_HiC.hic
MP_MamPri_Loxafr3.0_assisted_HiC_30.hic
MP_MamPri_ASM1433276v1_assisted_HiC_30.hic
MP_MamPri_ASM1433276v1_assisted_HiC.hic
MP_nonEtOH_Loxafr3.0_HiC.hic
MP_nonEtOH_Loxafr3.0_HiC_30.hic
MP_Loxafr3.0_HiC_30.hic
MP_Loxafr3.0_HiC.hic
PaleoHi-C_extended_reference.hic
direct_inversion_chr10_Loxafr3.0_HiC.hic
MiChroM_Loxafr3.0_HiC.hic
Woolly_Mammoth_Direct_Inv.sw
Woolly_Mammoth_MiChroM.sw


title: PaleoHi-C of Mammuthus primigenius DNA Zoo Sample6311, PeloHi-C lib id: 531


title: PaleoHi-C of Mammuthus primigenius DNA Zoo Sample6310, PeloHi-C lib id: A_mm_eth_501


title: thalamus,KO,thalamus_4

description: 10x Genomics

value: 1y 6m 7d


title: PaleoHi-C of Mammuthus primigenius DNA Zoo Sample6311, PeloHi-C lib id: 522


title: PaleoHi-C of Mammuthus primigenius DNA Zoo Sample6311, PeloHi-C lib id: 527


title: PaleoHi-C of Mammuthus primigenius DNA Zoo Sample6311, PeloHi-C lib id: 521


title: PaleoHi-C of Mammuthus primigenius DNA Zoo Sample6311, PeloHi-C lib id: 516


title: PaleoHi-C of Mammuthus primigenius DNA Zoo Sample6311, PeloHi-C lib id: 528


title: TPC1 cells, TFCP2L1 overexpression rep3

city: Guangzhou

first: Chuimian

last: Zeng

state: Guangdong

address: No.58, Zhongshan Road II

department: Department of Endocrinology

institute: The First Affiliated Hospital of Sun Yat-sen University

data_processing:
The libraries were sequenced on an illumina Novaseq 6000 platform and 150bp paired-end reads were generated.
Raw reads of fastq format were firstly processed using fastp and low quality reads were removed to obtain the clean reads.
Then clean reads for each sample were retained for subsequent analyses.
The clean reads were mapped to the reference genome using HISAT2.
FPKM of each gene was calculated and read counts of each gene were obtained by HTSeq-count.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM for each Sample

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer' s protocol.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer' s instructions.

value: papillary thyroid cancer cells

value: TFCP2L1 OE


title: thalamus,WT,thalamus_1

description: 10x Genomics


title: hypoxia_1_KYSE30

description:
OvsH_deg.xls
H1

value: oesophagus

value: esophageal squamous cell carcinoma


title: thalamus,WT,thalamus_2

description: 10x Genomics

value: WT


title: TPC1 cells, TFCP2L1 overexpression rep1


title: thalamus,KO,thalamus_3

description: 10x Genomics


title: PaleoHi-C of Mammuthus primigenius DNA Zoo Sample6311, PeloHi-C lib id: 515


title: TPC1 cells, TFCP2L1 overexpression rep2


title: PaleoHi-C of Mammuthus primigenius DNA Zoo Sample6311, PeloHi-C lib id: 510


title: PaleoHi-C of Mammuthus primigenius DNA Zoo Sample6311, PeloHi-C lib id: 509


title: PaleoHi-C of Mammuthus primigenius DNA Zoo Sample6311, PeloHi-C lib id: 504


title: whole_brain, KO,very_old_mouse_6_2

description: 10x Genomics


title: PaleoHi-C of Mammuthus primigenius DNA Zoo Sample6311, PeloHi-C lib id: 503


title: PaleoHi-C of Mammuthus primigenius DNA Zoo Sample6311, PeloHi-C lib id: 507


title: hypoxia_2_KYSE30

description:
OvsH_deg.xls
H2


title: whole_brain, KO,very_old_mouse_6_1

description: 10x Genomics


title: PaleoHi-C of Mammuthus primigenius DNA Zoo Sample6311, PeloHi-C lib id: 501


title: TPC1 cells, Vector rep3


title: PaleoHi-C of Mammuthus primigenius DNA Zoo Sample6310, PeloHi-C lib id: 524


title: PaleoHi-C of Mammuthus primigenius DNA Zoo Sample6310, PeloHi-C lib id: 523


title: PaleoHi-C of Mammuthus primigenius DNA Zoo Sample6310, PeloHi-C lib id: 518


title: whole_brain, WT,very_old_mouse_5_1

description: 10x Genomics


title: PaleoHi-C of Mammuthus primigenius DNA Zoo Sample6310, PeloHi-C lib id: 517


title: TPC1 cells, Vector rep1


title: PaleoHi-C of Mammuthus primigenius DNA Zoo Sample6310, PeloHi-C lib id: 512


title: resistant_R3-1,replicate 1, scRNA-Seq

city: New York

first: Itai

last: Yanai

state: NY

address: 435 East. 30th St.

institute: NYU Langone Health

description: expression counts for all samples from resistance experiment including untreated vehicles (V1, V2) and resistant tumors (R1.1, R1.2, R3.V, R3.1, R3.2). Sample ids are attached to cell barcode names (column names).

data_processing:
Raw reads were processed with the CellRanger v3.1.0 (10X genomics) pipeline using cellranger count command with default parameters and with the combined human hg38/GRCh38 and mouse mm10/GRCm39 genomes and Ensembl 93 and Ensembl 104 transcriptome references, respectively, which indicates the multi-species mode of cellranger to assign the human cells based on alignment quality. Cell barcodes assigned to the human genome were used for further analyses.
Assembly: hg38/GRCh38
Supplementary files format and content: pdx_persistence_counts_all.csv.gz , expression matrix for the PDX Parpi persistence experiment. Sample ids are attached to cell barcode names (column names). Cells were filtered based on expression of less than 20% of mitochondrial genes, more than 500 genes and more than 1000 umis expressed. Includes unfiltered protein coding genes.
Supplementary files format and content: pdx_resistance_counts_all.csv.gz, expression matrix for the PDX Parpi resistance experiment. Sample ids are attached to cell barcode names (column names). Cells were filtered based on expression of less than 20% of mitochondrial genes, more than 500 genes and more than 500 umis expressed. Includes unfiltered protein coding genes.

source_name: high grade serous ovarian cancer, patient derived xenograft

growth_protocol: Immunodeficient six-week-old female NOD SCID gamma (NSG) (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ) mice were purchased from Jackson Laboratory and allowed to acclimate to housing conditions. To generate HGSOC (High-Grade Serous Ovarian Cancer) PDX models of PARPi treatments, we used a previously characterized BRCA2 mutated tumor derived from PDX models (Cybulska et al. Am J. Pathol. 2018) (ID: 66799). Approximately 1×10^6 cells in a 1:1 ratio with Matrigel® Matrix (Corning, USA) were subcutaneously injected with a 27-gauge needle (BD Micro-Fine, USA) into the right lower mammary fat pad on the abdominal dorsal surface.

extract_protocol:
Tumors were minced with a razor blade and enzymatically dissociated in two steps. First, minced samples were incubated with 5 mL of digestion mix 1 (9 mL Advanced DMEM/F12, 1 mL Gentle Collagenase and 100 μL DNase I) at 37°C for 30 min, centrifuged at 1000 RPM for 4 min. After removing the supernatant, samples were incubated with 5 mL of digestion mix 2 (3 mL Advanced DMEM/F12, 2 mL Dispase, 5 mL TrypLE, 100 μL DNase I) at 37°C for 15 min, placed on a 70 μm cell strainer and washed with Advanced DMEM/F12 + 10% FBS. Samples were centrifuged at 1000 RPM for 4 min, incubated with 1 ml of ACK Lysing Buffer (ThermoFisher) for 4 min, washed with PBS + 10% FBS, resuspended in PBS, placed on a 35 μm cell strainer and viability was determined by Trypan Blue staining. Dissociated cells were collected for scRNA-Seq immediately (resistance experiment) or cryopreserved (dose-response experiment) by resuspending in freezing media (50% FBS, 40% Advanced DMEM/F12 and 10% DMSO) and stored at -80°C. Batches of replicates were processed on the same day. Frozen samples were thawed, washed in media, resuspended in PBS and the cell concentration adjusted for the 10X Genomics single-cell encapsulation protocol following library preparation and sequencing.
Library preparation was performed using the 10X Genomics Chromium platform with the Chromium Single Cell Library & Gel Bead Kit v3.1 following the manufacturer’s instructions.

treatment_protocol: To establish a drug-resistance model, tumors were treated along three passages. In a first passage, when the PDX tumors reached 100–200 mm3 tumor volume, Vehicle (10% dimethylacetamide, 5% Solutol HS15, 85% PBS) or talazoparib (0.0066mg per mouse = 0.33mg/kg, oral gavage) was administered for 5 consecutive days a week. Talazoparib treatment caused tumor remission and treatment was interrupted. Tumor sizes were followed until reappearance and treatment was reintroduced. Vehicles (V1 and V2) and drug treated tumors (R1.1 and R1.2) that did not show further regression upon re-treatment — thus indicating resistance — were collected for scRNA-Seq at the humane endpoint (1500-2000 mm3 or up to 20 mm in one dimension). A replicate tumor was implanted in a second passage and maintained under treatment upon tumor detection. The resulting tumor was implanted in a third passage, generating 3 replicates (2 talazoparib treated (R3.1 and R3.2) and 1 vehicle (R3.V)). In a second set of experiments aimed to study the persisters phenotype treated with different doses of talazoparib, mice were treated as described above with the following doses: a) Vehicle; b) Dose 1 (D1) was 0.13 mg/kg of talazoparib (Selleckchem, S7048) (n=2); c) Dose 2 (D2) was 0.23 mg/kg (n=2); d) Dose 3 (D3) was 0.33 mg/kg (n=2) and e) Dose 4 (D4) was 0.66 mg/kg. Vehicle tumors were collected at the humane endpoint and talazoparib treated tumors were collected after 50-57 days of treatment.

value: PDX nod-scid gamma (NSG) mice

value: epithelial

value: BRCA2 mutant

value: treated, talazoparib 0.33mg/kg


title: PaleoHi-C of Mammuthus primigenius DNA Zoo Sample6310, PeloHi-C lib id: 511


title: resistant_R3-2,replicate 2, scRNA-Seq

value: high grade serous ovarian cancer, patient derived xenograft


title: PaleoHi-C of Mammuthus primigenius DNA Zoo Sample6310, PeloHi-C lib id: 506

value: skin


title: resistant_R3-V,replicate 1, scRNA-Seq

value: untreated


title: whole_brain, KO,very_old_mouse_4_2

description: 10x Genomics

value: KO

value: 1y 7m 9d

value: M


title: whole_brain, WT,very_old_mouse_3_2

description: 10x Genomics


title: WJK-2878_HD13_repeat_CITE,Healthy Donor

first: Jahan

last: Rahman

state: New York

address: 417 E 68th St

department: Center for Hematologic Malignancies

institute: Memorial Sloan Kettering

library_source: other

data_processing:
Single cell RNA data were processed using Cellranger v6.0.2 count workflow to generate gene expression count matrices. Feature barcoding libraries were used to generate ADT count matrices and demultiplex cells/ perform cell-to-sample assignment with Cite-seq-count v1.4.5.  TCR data was processed using Cellranger’s vdj pipeline to generate cell-clonotype annotations.
Assembly: Human reference, GRCh38 (GENCODE v32/Ensembl 98)
Supplementary files format and content: Raw count matrices:  RNA_counts.csv.gz,HTO_counts.csv.gz, DCODE_counts.csv.gz
Supplementary files format and content: TCR annotations:  TCR_assignments.csv.gz
Library strategy: Single-cell immune profiling (RNA-Seq, surface proteomics, and TCR-seq)

molecule: protein

source_name: Peripheral Blood Mononuclear Cells

extract_protocol:
PBMCs were thawed, stained with a viability dye (GhostDye 510) and an antibody targeting CD45, and sorted for viable (GhostDye-negative), CD45+ cells.
Standard library construction was performed using a 10x Chromium Single Cell Immune Profiling Gel Bead Kit.

value: Peripheral Blood Mononuclear Cells

tag: library type

value: Dextramer/HTO

tag: dextramer-negative cells_hashed

value: Y


title: resistant_R1-2,replicate 2, scRNA-Seq


title: WJK-2878_HD13_repeat_RNA,Healthy Donor

value: mRNA


title: WJK-2878_HD13_repeat_TCR_VDJ,Healthy Donor

molecule: other

value: TCR-V(D)J


title: whole_brain, WT,very_old_mouse_3_1

description: 10x Genomics


title: WJK-2878_HD12_rep2_TCR_VDJ,Healthy Donor


title: WJK-2878_HD12_rep2_CITE,Healthy Donor


title: whole_brain,KO,very_old_mouse_2_2

description: 10x Genomics


title: TPC1 cells, Vector rep2

value: papillary thyroid cancer cells


title: vehicle_V2, replicate 2, scRNA-seq

value: untreated, vehicle


title: whole_brain, WT,very_old_mouse_5_2

description: 10x Genomics

value: WT


title: WJK-2878_HD12_rep2_RNA,Healthy Donor


title: WJK-2878_HD12_rep1_TCR_VDJ,Healthy Donor

value: N


title: WJK-2878_HD12_rep1_CITE,Healthy Donor


title: vehicle_V1, replicate 1, scRNA-seq

value: PDX nod-scid gamma (NSG) mice

value: epithelial

value: BRCA2 mutant


title: whole_brain,KO,very_old_mouse_2_1

description: 10x Genomics


title: PaleoHi-C of Mammuthus primigenius DNA Zoo Sample6310, PeloHi-C lib id: 505

value: skin

value: EtOH-preserved on site


title: kura_T40

description: tables containing detected copy number alterations and single nucleotide variants. Annotations are relative to a reference sample in the second column (Ex: REFERENCE:SUBJECT) refers to a reference sample

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software. The FASTQ files were processed using the Seq-N-Slide pipeline (https://doi.org/10.5281/zenodo.5550459). Adapter sequences were trimmed with Trimmomatic and then aligned to the human reference genome (build hg38/GRCh38) using the Burrows-Wheeler Aligner with the BWA-MEM algorithm.
Low confidence mappings (mapping quality < 10) and duplicate reads were removed using Sambamba. Further local indel realignment and base-quality score recalibration were performed using the Genome Analysis Toolkit (GATK). Copy number profiles were calculated using Control-FREEC with untreated samples as the matched controls. ANNOVAR was used to annotate variants with genomic context such as functional consequence on genes and identify presence in public variant databases gnomAD and COSMIC.
Assembly: hg38/GRCh38
Supplementary files format and content: Kuramochi_WES_CNVs.tsv, tsv, list of copy number alterations relative to a specified reference sample (Ex column 2: REFERENCE:SUBJECT)
Supplementary files format and content: Kuramochi_WES_SNVs.tsv, tsv, list of single nucleotide variants relative to a specified reference sample.
Library strategy: WES (whole exome sequencing)

source_name: Cell line

growth_protocol: Cells were cultured in RPMI-1640 (ThermoFisher) with 10% Fetal Bovine Serum (FBS), 1% MEM Non-Essential Amino Acids, 1% L-Glutamine 200 mM, 1% Antibiotic-Antimycotic solution 100X and 0.25 U/mL insulin solution (Sigma-Aldrich)

extract_protocol:
Cells were trypsinized and single-cell suspensions were counted. Genomic DNA extraction for whole exome sequencing was performed using Qiagen Blood and Cell DNA kit (Catalog no: 13323).
The extracted DNA from representative samples (C, T10, T40 and T320) was sent to the Broad Institute facility and processed according to the in-house pipeline. Briefly, 125ng in 50μL was prepared for sequencing using the KAPA Hyper Prep Kit. Hybridization and capture were performed using the relevant components of IDT’s XGen hybridization and wash kit and following the manufacturer’s suggested protocol. Sequencing was performed using Illumina Novaseq.

treatment_protocol: Kuramochi cells were treated in dose escalation from 1uM to 320uM of olaparib, generating populations resistant to a range of doses plus untreated control (C). The cells resistant to 10 uM (T10), 40 uM (T40) and 320 uM (T320) plus untreated control (C) were collected for whole exome sequencing.

value: Cell line

value: Kuramochi

value: Epithelial

value: untreated and treated cells with 10uM or 320uM of olaparib


title: whole_brain, KO,very_old_mouse_4_1

description: 10x Genomics

value: KO

value: 1y 7m 9d

value: M


title: whole_brain,WT,very_old_mouse_1_1

description: 10x Genomics

value: 1y 7m 1d


title: WJK-2876_ZRSR2_6_RNA,ZRSR2 Mutant

value: Peripheral Blood Mononuclear Cells

value: mRNA

value: Y


title: WJK-2878_HD12_rep1_RNA,Healthy Donor

value: N


title: WJK-2876_ZRSR2_6_CITE,ZRSR2 Mutant

value: Dextramer/HTO


title: WJK-2876_ZRSR2_6_TCR_VDJ,ZRSR2 Mutant

value: TCR-V(D)J


title: whole_brain,WT,very_old_mouse_1_2

description: 10x Genomics

value: WT


title: left_hemisphere,KO,old_mouse_6

description: 10x Genomics


title: WJK-2876_ZRSR2_5_r2_TCR_VDJ,ZRSR2 Mutant


title: resistant_R1-1,replicate 1, scRNA-Seq

value: high grade serous ovarian cancer, patient derived xenograft

value: PDX nod-scid gamma (NSG) mice

value: epithelial

value: BRCA2 mutant

value: treated, talazoparib 0.33mg/kg


title: WJK-2876_ZRSR2_5_r2_RNA,ZRSR2 Mutant


title: WJK-2876_ZRSR2_5_r1_TCR_VDJ,ZRSR2 Mutant


title: kura_C

value: Cell line

value: Kuramochi

value: Epithelial

value: untreated and treated cells with 10uM or 320uM of olaparib


title: WJK-2876_ZRSR2_5_r2_CITE,ZRSR2 Mutant


title: left_hemisphere,KO,old_mouse_5

description: 10x Genomics

value: KO

value: M


title: WJK-2876_ZRSR2_5_r1_RNA,ZRSR2 Mutant

value: Peripheral Blood Mononuclear Cells

value: mRNA


title: WJK-2876_ZRSR2_5_r1_CITE,ZRSR2 Mutant

value: Y


title: keratinocytes, cultured, Patient 3

city: Nagoya

first: Takuya

last: Takeichi

address: 65 Tsurumai-cho, Showa-ku

country: Japan

institute: Nagoya University Graduate of School

description: 10x Genomics

data_processing:
Preparation of the scRNAseq library, sequencing, and data preprocessing were outsourced to Azenta Corp., Japan branch, as previously described, with slights modifications. Research Square [https://doi.org/10.21203/rs.3.rs-2513325/v1]
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Skin

growth_protocol: 1- to 2-cm2 skin samples were taken under local anesthesia from areas suspected of having RM. The tissue was placed in culture medium and sent to Japan Tissue Engineering Co., Ltd. (J-TEC, Gamagori, Japan). After the subcutaneous tissue was removed, the tissue was minced and trypsinized. The cells were cocultured with lethally irradiated 3T3-J2 cells. After 3 weeks of culturing, some subconfluent cultures were frozen, preserved, and later subcultured. In this way, secondary subcultures could be prepared later for use as grafts. The confluent keratinocytes were detached from the tissue-culture dish with dispase and brought to the bedside in serum-free medium.

extract_protocol:
Dead cells and debris were removed using the Dead Cell Removal Kit (Miltenyi Biotec). Each single-cell suspension (viability of samples >93%) was subjected to scRNAseq.
10x scRNA-Seq/Illumina-compatible

treatment_protocol: CEA products (passages 3-4) from Patient 2 and PAtient 3 were obtained from J-TEC. Two specimens of cultured normal human epidermal keratinocytes (healthy control 1: lot#08138, 57-year-old, female, abdomen, Caucasian (Kurabo); healthy control 2: KER110013, 44-year-old, female, abdomen, Caucasian (KAC)) as controls were purchased from Kurabo (Osaka, Japan) and KAC Co., Ltd. (Amagasaki, Japan), respectively.

value: Skin

value: keratinocytes


title: kura_T320


title: left_hemisphere,WT,old_mouse_3

description: 10x Genomics

value: WT


title: WJK-2870_ZRSR2_4_RNA,ZRSR2 Mutant


title: WJK-2870_ZRSR2_4_CITE,ZRSR2 Mutant

value: Dextramer/HTO


title: left_hemisphere,WT,old_mouse_2

description: 10x Genomics


title: left_hemisphere,KO,old_mouse_4

description: 10x Genomics


title: WJK-2870_ZRSR2_1_repeat_TCR_VDJ,ZRSR2 Mutant

value: TCR-V(D)J


title: keratinocytes, cultured, healthy control 2

description: 10x Genomics

value: wild type


title: WJK-2870_ZRSR2_1_repeat_CITE,ZRSR2 Mutant


title: kura_T10


title: WJK-2870_ZRSR2_1_repeat_RNA,ZRSR2 Mutant


title: left_hemisphere,WT, old_mouse_1

description: 10x Genomics


title: keratinocytes, cultured, healthy control 1

description: 10x Genomics


title: WJK-2866_SRSF2_13_RNA,SRSF2 Mutant


title: WJK-2866_SRSF2_13_TCR_VDJ,SRSF2 Mutant


title: hippocampus, HET, mouse5

description: 10x Genomics

source_name: hippocampus

value: hippocampus

value: HET

value: F


title: WJK-2866_SRSF2_12_TCR_VDJ,SRSF2 Mutant


title: Adipose Tissue, HIV+DM, 3037

city: Nashville

first: Samuel

last: Bailin

address: 1161 21st Avenue South, MCN A-2200

institute: Vanderbilt Universit Medical Center

data_processing:
Samples were sequences in two batches on the Illumina NovaSeq 6000 platform using paired-end sequencing (2 x 150 pb)
Read quality was assessed and adapter read-through sequences were removed using fastp
Reads were mapped to the Human GENCODE release 34 hg38 using STAR v2.7.3a
FeatureCounts was used to assign reads to features using GENCODE v34 annotation
Assembly: GENCODE release 34 GRCh38
Supplementary files format and content: text file with raw counts from featureCounts

source_name: subcutaneous adipose tissue

extract_protocol:
Total RNA was extracted from subcutaneous adipose tissue using Qiagen RNeasy Lipid Tissue Kit after mechanical lysis.
cDNA libraries were prepared with NEBNext Ultra II Directional RNA Library Prep Kits

value: subcutaneous adipose tissue

value: Male

tag: disease state

value: HIV+ diabetic


title: WJK-2866_SRSF2_12_RNA,SRSF2 Mutant


title: cortex, HET, mouse2

description: 10x Genomics

source_name: cortex

value: cortex


title: WJK-2870_ZRSR2_4_TCR_VDJ,ZRSR2 Mutant


title: Adipose Tissue, HIV+DM, 3039


title: WJK-2866_SRSF2_12_CITE,SRSF2 Mutant


title: hippocampus, HET, mouse2

description: 10x Genomics


title: WJK-2864_SRSF2_10_TCR_VDJ,SRSF2 Mutant


title: Adipose Tissue, HIV+DM, 3034


title: WJK-2864_SRSF2_10_RNA,SRSF2 Mutant


title: WJK-2864_SRSF2_10_CITE,SRSF2 Mutant


title: SrcX_Sc4_KO_skin_TK341s8

city: Vienna

first: Thomas

last: Weichhart

address: Waehringerstraße 10

department: Center for Pathobiochemistry and Genetics

country: Austria

institute: Medical University of Vienna

data_processing:
Demultiplxing, alignment, feature counting and filtering was performed with the 10x Genomics Cell Ranger pipeline version 5.0.1 against reference transcriptome mm10-2020-A.
Assembly: GRCm38 (UCSC mm10)
Supplementary files format and content: FASTQ files
Supplementary files format and content: 10x Genomics Cell Ranger fitered matrix HDF5

extract_protocol: 10x Genomic Single Cell 3' v3

value: skin

value: skin cell suspension

value: Tsc2fl/fl CD11c-cre

value: female


title: WJK-2859_SRSF2_9_CITE,SRSF2 Mutant

value: Peripheral Blood Mononuclear Cells

value: Y


title: WJK-2866_SRSF2_13_CITE,SRSF2 Mutant


title: Adipose Tissue, HIV+DM, 3033


title: Adipose Tissue, HIV+DM, 3032


title: cortex, HET, mouse5

description: 10x Genomics


title: WJK-2859_SRSF2_9_RNA,SRSF2 Mutant

value: mRNA


title: WJK-2854_SRSF2_7_TCR_VDJ,SRSF2 Mutant


title: SrcX_Sc3_KO_skin_TK341s7


title: Adipose Tissue, HIV+DM, 3031

value: Female


title: WJK-2854_SRSF2_7_CITE,SRSF2 Mutant

value: Dextramer/HTO


title: SrcX_Sc1_WT_skin_TK341s5


title: WJK-2854_SRSF2_7_RNA,SRSF2 Mutant


title: WJK-2765_SRSF2_5_replicate_2_TCR_VDJ,SRSF2 Mutant

value: TCR-V(D)J

value: N


title: Adipose Tissue, HIV+DM, 3030


title: Adipose Tissue, HIV+DM, 3035


title: WJK-2765_SRSF2_5_replicate_2_CITE,SRSF2 Mutant


title: WJK-2765_SRSF2_5_replicate_2_RNA,SRSF2 Mutant


title: Adipose Tissue, HIV+DM, 3029


title: liver CD45+ cells, pex2 KO, Rep1

city: Halifax

first: Francesca

last: Di Cara

state: Nova Scotia

address: 5850/5980 University Avenue

country: Canada

institute: Dalhousie University

description:
Instrument model used (Illumina NovaSeq X Plus) was not available in drop down menu
10X Genomics

data_processing:
Demultiplexing,barcode processing, gene counting and aggregation were made using the cell ranger multi pipeline in Cell Ranger software v.7.0.0.
Assembly: mm10
Supplementary files format and content: Tab-separated values and matrix files

extract_protocol:
Postnatal day-0 mice from three genotypes (Pex2-/-, Pex2Het, and WT) were euthanized by decapitation, their livers were excised and passed through a 70 μm cell strainer (Falcon Cat#352350) into 1x HBSS (Gibco Cat#14025-092)using a 1 mL syringe plunger. Liver cell suspensions were then centrifuged at 20 xg for 5 min to remove hepatocytes. The supernatant was isolated and cells were treated with Ammonium-Chloride-Potassium (ACK) Lysing Buffer to lyse red blood cells, and then washed. The final cell suspension was resuspended in 1x PBS 0.5% BSA, cell counts were determined and surface-stained using a 1:50 dilution of FITC- and ef450-conjugated anti-CD45 antibodies (BioLegend Cat#103108 and ThermoFisher eBioscence Cat#48-0451-82), and staining with a fixable viability dye (ThermoFisher eBioscience Cat#65-0865). Viable CD45+ cells were sorted by Fluorescence-activated cell sorting (FACs) on a BD FACs ARIA II cell sorter.
Sorted CD45+ cells were processed and fixed according to the 10X Genomics Flex Assay protocol using the Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (10X Genomics Cat#PN-1000414). Fixed cells were counted and stored at -80oC and shipped on dry ice to the Princess Margaret Genomics Centre, Toronto Ontario, Canada for the generation of barcoded libraries using the Chromium Fixed RNA Kit, Mouse Transcriptome (10X Genomics Cat#PN-1000495) and Dual Index Kit TS Set A 96 rxns (10X Genomics Cat#PN-1000251) prior to sequencing.

value: liver

value: CD45+ cells

tag: age

value: postnatal day 0


title: WJK-2765_SRSF2_5_replicate_1_TCR_VDJ,SRSF2 Mutant


title: liver CD45+ cells, pex2 Het, Rep 1

value: pex2-/+ (Het)


title: WJK-2859_SRSF2_9_TCR_VDJ,SRSF2 Mutant


title: WJK-2765_SRSF2_5_replicate_1_CITE,SRSF2 Mutant


title: Adipose Tissue, HIV+DM, 3028

value: subcutaneous adipose tissue

value: Male

value: HIV+ diabetic


title: WJK-2726_SRSF2_3_TCR_VDJ,SRSF2 Mutant


title: WJK-2765_SRSF2_5_replicate_1_RNA,SRSF2 Mutant


title: liver CD45+ cells, pex2 WT, Rep 1


title: WJK-2726_SRSF2_3_CITE,SRSF2 Mutant


title: Brain_Contra_Stroke_3day_HTO

first: Barry

middle: W

last: McColl

address: 49 Little France Crescent

department: Centre for Discovery Brain Sciences

data_processing:
Count matrices were generated for each library using the 10X Genomics CellRanger v3.0.2 pipeline. First, raw reads were demultiplexed to produce fastq files. Second, reads were aligned to the mouse reference genome (GRCm38) and quantified. Resultantly, two unique molecule identifiers (UMI) based expression matrices were generated each for the ipsilateral and contralateral conditions which were pre-processed and analysed using the Seurat v3 package in R
Assembly: GRCm38
Supplementary files format and content: Seurat object

source_name: Brain

extract_protocol:
Cells were extracted from brains using a no-enzyme cold processing approach in Hank's balanced salt solution to avoid activation of immune cells due to warm enzyme processing.
Single cell 3’ gene expression (mRNA) and cell surface hashtag-oligonucleotide (HTO) libraries were prepared according to the Chromium Single Cell 3ʹ with Feature Barcoding technology for Cell Surface Protein Reagent Kit v3 protocol (10X Genomics) with modifications for incorporation of TotalSeq™-A HTO antibodies (clones M1/42; 30-F11, BioLegend). Briefly, generation of gel beads in emulsion (GEM) partitioned with single cells, reverse transcription to generate cDNA and HTO-barcoded DNA, and DNA amplification were performed according to manufacturer instructions with the addition of HTO primers during DNA amplification. Amplified cDNA and HTO-derived DNA were separated by size selection, fragmented and libraries constructed.

value: Brain

value: Immune cells

value: WT


title: SrcX_Sc2_WT_skin_TK341s6

value: skin

value: skin cell suspension

value: female


title: Adipose Tissue, HIV+DM, 3027


title: WJK-2719_SRSF2_2_TCR_VDJ,SRSF2 Mutant

value: Peripheral Blood Mononuclear Cells

value: Y


title: WJK-2726_SRSF2_3_RNA,SRSF2 Mutant

value: mRNA


title: WJK-2719_SRSF2_2_CITE,SRSF2 Mutant

value: Dextramer/HTO


title: Adipose Tissue, HIV+DM, 3026


title: Brain_Contra_Stroke_3day_Cells


title: Brain_Ipsi_Stroke_3day_HTO


title: WJK-2719_SRSF2_2_RNA,SRSF2 Mutant


title: WJK-2707_SRSF2_1_TCR_VDJ,SRSF2 Mutant

value: TCR-V(D)J

value: N


title: WJK-2707_SRSF2_1_CITE,SRSF2 Mutant


title: Adipose Tissue, HIV+DM, 3024


title: Brain_Ipsi_Stroke_3day_Cells


title: WJK-2707_SRSF2_1_RNA,SRSF2 Mutant


title: Adipose Tissue, HIV+DM, 3023


title: Adipose Tissue, HIV+DM, 3022


title: APPNL-G-F mouse with exercise, hippocampus, snRNAseq

first: Zheng

last: Sun

state: Texas

address: 1329 Moursund St

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0
Assembly: mm10
Supplementary files format and content: Tab-separated bacode files
Supplementary files format and content: Tab-separated feature files
Supplementary files format and content: Tab-separated matrix files

source_name: Hippocampus

growth_protocol: Eight-week old female WT and NLGF C57BL/6J mice were fed ab lib with normal chow diet

extract_protocol:
Hippocampus was isolated immediately on ice, washed with cold D-PBS, and snap-frozen with liquid nitrogen. The Frankenstein' protocol was adopted to isolate the nuclei from frozen tissues (https://www.protocols.io/view/frankenstein-protocol-for-nuclei-isolation-from-f-5jyl8nx98l2w/v2).
Chromium NextGEM SingleCell 3-_GeneExpression_v3.1_DualIndex

treatment_protocol: Mice were housed in cages with running wheel for voluntary exercise for 10 weeks.

value: Hippocampus

value: Female

value: APPNL-G-F

value: Exercise


title: APPNL-G-F mouse without exercise, hippocampus, snRNAseq

value: No


title: Adipose Tissue, HIV+DM, 3021

value: subcutaneous adipose tissue

value: HIV+ diabetic


title: keratinocytes, cultured, Patient 2

description: 10x Genomics

value: Skin

value: keratinocytes

value: KRT1 c.559C>T p.(Leu187Phe)


title: Brain_20Gy_ 5 days_3

type: RNA

city: St Paul

first: Davis

last: Seelig

state: MN

address: 1352 Boyd Ave.

department: Department of Veterinary Clinical Sciences

institute: University of Minnesota

description: 100ng of RNA was used for NanoString nCounter Glial Profiling Panel

hyb_protocol: A total of 100 nanograms of RNA from each sample was used to evaluate gene expression by the nCounter® Glial Profiling Panel from NanoString (NanoString Technologies, Seattle, WA, USA) following manufactures protocol (MAN-10023-11 nCounter XT Assay User Manual).

scan_protocol: A total of 100 nanograms of RNA from each sample was used to evaluate gene expression by the nCounter® Glial Profiling Panel from NanoString (NanoString Technologies, Seattle, WA, USA) following manufactures protocol (MAN-C0035-07, nCounter Analysis System Manual).

data_processing: The nSolver™ Analysis Software version 4.0 (NanoString Technologies, Seattle, WA, USA) quality control parameters were used to assess quality of imaging, binding density, positive control linearity and positive control limit of detection. The nSolver™ Analysis Software Advanced Analysis Module (version 2.0.134) was used to analyze gene expression data, including gene normalization, and differential expression volcano plots with p-values from linear regression. Three mice highlighted above (13-1, G14-7 and G13-5) were removed from Advanced Analysis Module due to high binding densities (over 2.8) which was causing suppressed counts in lower expressed genes. The Advanced Analysis Module was used to normalize raw gene data for each sample to the geometric mean of the endogenous housekeeping genes using the geNorm algorithm. The normalized gene expression data was analyzed using 10.1.2 (GraphPad Software, San Diego, CA,USA). One-way analysis of variance (ANOVA) with the Dunnett  post-hoc test was used to evaluate differences between treatment groups and control mice.

extract_protocol: RNA was extracted using the RNeasy Plus Universal Mini kit (Qiagen, Germantown, MD, Cat# 73404) according to manufactures instructions.

treatment_protocol: SKH1 mice were treated with 20Gy or 30Gy hindlimb radation (RT).  Brains were collected and frozen from 3 mice per group including control group (no treatment). RNA was extracted from the frozen brain tissue.

value: Brain

tag: gender

tag: time point

value: 5 days


title: Brain_20Gy_ 5 days_2

tag: tissue


title: WT mouse with exercise, hippocampus, snRNAseq

value: WT


title: Adipose Tissue, HIV+DM, 3025

value: Male


title: Brain_20Gy_ 5 days_1


title: Brain_20Gy_ 24 hours_3

value: 24 hours


title: Brain_20Gy_ 24 hours_2


data_processing:
Sorted BAM file was made by Cell Ranger software v3.1.0.
Then we used snaptools to generate the bin-by-nuclei matrix for APP_EX, APP_RT, WT_EX, and W_TRT samples separately.
All four sample were then combined for analysis with the package snapATAC following the pipeline tutorial https://github.com/r3fang/SnapATAC/blob/master/examples/10X_brain_5k/README.md. Original filters of nuclei were set as: UMI >= 3 & <= 5; promoter_ratio >= 0.15 & <= 0.6; peak_region_fragments > 1,000  & < 20,000; frag_in_peak_ratio > 0.15. Bins in blacklist or mitochondrial chromatin or over top 95% coverage among all bins were filtered out. Next, dimensionality reduction was done with the function runDiffusionMaps with num.eig set as 50. Then clustering was done with the function runKNN (eigs.dims set as 1:30 and k as 15) and the function runCluster (leiden version 0.3.5 and resolution as 1.5). Then bins were binarized for further analysis. Peaks were then called on bins in each cluster with buffer.size set as 500. Peaks were then merged by the function reduce. Lastly, peaks were scaled by the function scaleCountMatrix with the RPM method.
The peak-by-nuclei matrix filtered were provided here as processed data files.
Assembly: mm10
Supplementary files format and content: Tab-separated bacode files
Supplementary files format and content: Tab-separated feature files
Supplementary files format and content: Tab-separated matrix files

extract_protocol:
Hippocampus was isolated immediately on ice, washed with cold D-PBS, and snap-frozen with liquid nitrogen. The Frankenstein' protocol was adopted to isolate the nuclei from frozen tissues (https://www.protocols.io/view/frankenstein-protocol-for-nuclei-isolation-from-f-5jyl8nx98l2w/v2).
Chromium_NextGEM_SingleCell_ATAC v2


title: Adipose Tissue, HIV+DM, 3019


title: Brain_20Gy_ 24 hours_1


title: WT mouse without exercise, hippocampus, snRNAseq


title: Brain_30Gy_ 24 hours_3


title: Adipose Tissue, HIV+DM, 3018


title: Adipose Tissue, HIV+DM, 3012


title: Brain_Control_ 24 hours_3

value: Control


title: Brain_Control_ 24 hours_2


title: Adipose Tissue, HIV+DM, 3011


title: Brain_Control_ 24 hours_1


title: Brain_20Gy_12 days_3

value: 12 days


title: Brain_20Gy_12 days_2


value: Hippocampus


title: Brain_30Gy_12 days_2

value: Female


title: Adipose Tissue, HIV+DM, 3010


title: Brain_30Gy_12 days_1


title: Sample 4_G0IFNg

city: Bethesda

first: Teruhiko

last: Yoshida

state: Maryland

address: 10 Center Drive, 9N208

department: NIDDK - KDB

institute: National Institutes of Health

data_processing:
Illumina RTA v3.4.4 software was used fro base calling, Bcl2fastq v2.20 was used for sample demultiplexing
The analysis was performed with the Cell Ranger v6.1.2 software using the default parameters with premRNA analysis turned on. The reference was built from mm10 reference genome, HIV-1 virus sequence and APOL1 gene added.
Assembly: mm10 and HIV-1: NC_001802.1 and APOL1
Supplementary files format and content: tar.gz files contain filtered_features_bc_matrix folder output from CellRanger Count

source_name: Mouse Kidney Glomeruli

extract_protocol:
Nuclei from isolated five glomeruli sample types (WT, G0xTg26, G1xTg26, G0+interferon-g, G1+interferon-g) were prepared. Snap frozen isolated glomeruli were lysed in EZlysis buffer (#NUC101-1KT, Sigma, Darmstadt, Germany) and homogenized 30 times using a loose Dounce homogenizer and 5 times in a tight pestle. After 5 min incubation, the homogenate was passed through a 40 µm filter (43-50040, PluriSelect, El Cajon, CA) and centrifuged at 500g at 4°C for 5 min. The pellet was washed with EZlysis buffer and again centrifuged at 500g at 4°C for 5 min. The pellet was resuspended with DPBS with 1% FBS and passed through a 5 µm filter (43-50005, PluriSelect) to make final nuclei prep for loading on to a 10x Chromium Chip G (10X Genetics, Pleasanton, CA) for formation of gel beads in emulsion (GEM).
10x Genomics Chromium 3’ V3.1 mRNA-seq library protocol

treatment_protocol: We collected glomeruli from 9 to 12-week-old mice. For interferon-g model experiments, we injected a single dose of recombinant murine interferon-g (CYT-358, ProSpec, East Brunswick NJ) in phosphate-buffered saline (PBS) at 1.125 × 107 U/kg body weight, retro-orbitally under isoflurane anesthesia (0 hour) and glomeruli were extracted 24 hours after the interferon-g administration.

value: Kidney Glomeruli

value: interferon-g


title: Brain_30Gy_ 24 hours_2


title: Brain_Control_12 days_3


value: APPNL-G-F

value: No


title: Adipose Tissue, HIV+DM, 3008

value: subcutaneous adipose tissue

value: HIV+ diabetic


title: Sample 3_G1Tg26


title: Adipose Tissue, HIV+DM, 3020


title: Adipose Tissue, HIV+DM, 3009


title: Iris,Dorsal,4dpl,Rep3 [4dpl_3]

city: Baltimore

first: Seth

last: Blackshaw

state: MD

address: 733 N Broadway

department: Neuroscience

institute: Johns Hopkins University

data_processing:
Reads were quality trimmed using Trim Galore with parameters --stringency 3 --paired --length 36.
Transcript expression was quantified using salmon with parameters -l ISR --validateMappings -p 12 --numGibbsSamples 20 --seqBias --gcBias -d. Samples with alignment rates > 80% were included in downstream analysis.
Assembly: PWaltl_transcriptome.fasta
Supplementary files format and content: avgTPM.csv contains average TPM values of inferential replicates for each sample
Supplementary files format and content: PWaltl_transcriptome.fasta contains transcriptome used for quantification

organism: Pleurodeles waltl

source_name: dorsal iris tissue

extract_protocol:
Dorsal iris tissue was dissected from 13-month-old newts using intact or lentectomized animals. Tissue from 4 animals were pooled for each biological replicate, collected in triplicate. Samples were collected into cold TRI Reagent (Zymo, R2050-1-50), vortexed, and stored at -80 °C until RNA extraction. RNA isolation was performed via extraction with 0.2 volumes chloroform followed by processing of the aqueous phase with the Direct-zol RNA Microprep Kit (Zymo, R2060) according to manufacturer’s instructions, including an in- column DNase I treatment.
RNAseq libraries were prepared using 72-130 ng of isolated RNA, using NEBNext® UltraTM II Directional RNA Library Prep with Sample Purification Beads (NEB, E7765S) and NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490S). Indexing was performed using NEBNext® Multiplex Oligos for Illumina® (NEB, E7500/7710/7730).

treatment_protocol: Anesthesia via 0.1% tricaine followed by surgical lentectomy.

value: dorsal iris tissue


title: Adipose Tissue, HIV+DM, 3007


title: Brain_30Gy_ 24 hours_1


title: Brain_Control_12 days_2


title: Iris,Dorsal,4dpl,Rep2 [4dpl_2]


title: Brain_30Gy_ 5 days_3


title: Iris,Dorsal,4dpl,Rep1 [4dpl_1]


title: Sample 2_G0Tg26


title: Iris,Dorsal,1dpl,Rep3 [1dpl_3]


title: Sample 1_WT


title: Brain_30Gy_ 5 days_1


title: Adipose Tissue, HIV+DM, 3006


title: 34_G2_Tg_4

data_processing:
Illumina RTA v3.4.4 software was used fro base calling, Bcl2fastq v2.17 was used for sample demultiplexing
Adapters from the samples were trimmed using Cutadapt 1.18 software
Genome mapping and transcript annotation were using STAR v2.7.0f with reference genome mm10.
The gene expression quantification analysis was performed for all samples using RSEM 1.3.1
Assembly: mm10 and HIV-1: NC_001802.1 and APOL1
Supplementary files format and content: xlsx file contains rawcount matrix from RSEM

extract_protocol:
Isolated glomerular tissues from 8 line (WT, G0, G1, G2, Tg26, G0xTg26, G1xTg26, G2xTg26; n=5, 3, 4, 3, 5, 5, 5, 4, respectively) were homogenized in QIAzol. Total RNA was extracted using RNeasy Plus Universal Kit (73404, QIAGEN) following the manufacturer’s protocol, including removal of genomic DNA. RNA samples were prepared sequencing at the sequencing facility, Frederick National Laboratory for Cancer Research, NCI, Frederick, MD.
RNA libraries were prepared for sequencing using standard Illumina TruSeq Stranded mRNA library protocol.

treatment_protocol: All mouse glomerular samples were collected between 9 weeks and 12 weeks of age.


title: Adipose Tissue, HIV+DM, 3005


title: Iris,Dorsal,Intact,Rep3 [IRIS_3]

value: Intact


title: Sample 5_G1IFNg


title: Iris,Dorsal,Intact,Rep2 [IRIS_2]


title: 33_G2_Tg_3


title: Adipose Tissue, HIV+DM, 3003


title: Brain_30Gy_ 5 days_2

value: Brain


title: RNAseq_DDMLLENL_E4_noShield1_differentated

city: Planegg

first: Anna

last: Danese

address: Grosshaderner strasse 9

country: Germany

institute: Ludwig Maximilians University

data_processing:
bcl2fastq
read trimming to 100 bp length using homerTools trim
STAR aligner
Assembly of the table in R
Assembly: GRCh38
Supplementary files format and content: ReadsPerGene.txt
Supplementary files format and content: tab separated text file containing 7 columns. 1st contains the gene annotation, 2-7 contains the raw counts per sample

source_name: Macrophages

extract_protocol:
RNeasy Plus Mini Kit (Qiagen)
Illumina TruSeq Stranded total RNA

tag: cell type

value: Macrophages

value: Retrovirally transduced

value: Differentiation


title: RNAseq_DDMLLENL_E7_noShield1_differentated

tag: genotype


title: RNAseq_DDMLLENL_E7_plusShield1

source_name: Monocytic progenitors

value: Monocytic progenitors

value: Expansion/Cultivation


title: 32_G2_Tg_2

value: Control


title: RNAseq_DDMLLENL_E4_plusShield1


title: Adipose Tissue, HIV+DM, 3001


title: 31_G2_Tg_1


title: RNAseq_DDMLLENL_E3_plusShield1


title: RNAseq_DDMLLENL_E3_noShield1_differentated


title: Adipose Tissue, HIV+DM, 3002

value: Male


title: Adipose Tissue, HIV+preDM, 2124

value: HIV+ prediabetic


title: HEL cells, LRCherry2.1-sgDCAF15#2, rep1

city: Philadelphia

first: Luca

last: Busino

state: Pennsylvania

address: 421 Curie Boulevard

department: Cancer Biology

institute: University of Pennsylvania

description:
D15.hic
D15.mcool

data_processing:
Hi-C reads were combined between replicates and aligned to the human hg19 genome with Juicer, using an annotation file based on the Arima restriction enzymes and default settings
Contact matrices were generated by Juicer in .hic format using Knight-Ruiz (KR) normalization, and converted to .cool format at various resolutions using the hicConvertFormat function in HiCExplorer
Assembly: hg19
Supplementary files format and content: hic, mcool

source_name: HEL

growth_protocol: HEL human acute myeloid leukemia cells were maintained in RPMI-1640 media supplemented with 10% fetal bovine serum (FBS) and 1% Penicillin/Streptomycin in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Hi-C was performed on cells using the Arima High Coverage HiC Kit (Arima Genomics, A101030), following all manufacturer instructions
Hi-C libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (New England BioLabs, E7645S) and NEBNext Dual Index Primers (New England BioLabs, E7600S), with modifications to the protocol as specified by the Arima High Coverage HiC Kit

treatment_protocol:
Prior to experiment, HEL cells were engineered to stably express SpCas9 protein
Additionally, prior to experiment, SpCas9-expressing HEL cells were lentivirally-infected with the LRCherry2.1 vector containing an sgRNA targeted against ROSA26(Control) or DCAF15, and cells were sorted for mCherry positivity

tag: cell line

value: HEL

value: acute myeloid leukemia


title: Iris,Dorsal,1dpl,Rep1 [1dpl_1]

tag: treatment


title: Iris,Dorsal,1dpl,Rep2 [1dpl_2]


title: Adipose Tissue, HIV+preDM, 2123


title: HEL cells, LRCherry2.1-sgDCAF15#2, rep2

description:
D15.hic
D15.mcool


title: Adipose Tissue, HIV+DM, 3004


title: 29_G1_Tg_4

value: Kidney Glomeruli


title: HEL cells, LRCherry2.1-sgROSA26(Control), rep2

description:
Rosa.hic
Rosa.mcool

value: WT


title: 27_G1_Tg_2


title: HEL cells, LRCherry2.1-sgROSA26(Control), rep1

description:
Rosa.hic
Rosa.mcool


title: Adipose Tissue, HIV+preDM, 2122

value: subcutaneous adipose tissue

value: Female


title: HEL cells, LRCherry2.1-sgDCAF15#2, total-SMC3, ChIP

data_processing:
fastq files were aligned with BOWTIE2
Reads were sorted and duplicates removed with SAMTOOLS
Peaks were called with Macs2
Further analysis was performed in RStudio using the R packages Rsamtools, DESeq2, GenomicAlignments, soGGi, ggplot2, and profileplyr
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
Cells were fixed with 1% paraformaldehyde in PBS for 10minutes; after quenching and cell lysis, chromatin was sonicated using a Covaris Ultrasonicator
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA library prep with sample purification beads (NEB, E7103S) following the manufacturer’s instructions

tag: chip antibody

value: total-SMC3 (Bethyl Laboratories, A300-060A)


title: Iris,Dorsal,Intact,Rep1 [IRIS_1]

value: dorsal iris tissue

value: Intact


title: HEL cells, LRCherry2.1-sgDCAF15#2, acetyl-SMC3, ChIP

value: acetyl-SMC3 (Lys105/106) (EMD Millipore, MABE1073)


title: Adipose Tissue, HIV+preDM, 2121


title: 30_G1_Tg_5


title: HEL cells, LRCherry2.1-sgROSA26(Control), acetyl-SMC3, ChIP


title: HEL cells, LRCherry2.1-sgROSA26(Control), Input


title: 25_G0_Tg_5


title: HEL cells, LRCherry2.1-sgROSA26(Control), total-SMC3, ChIP


title: 26_G1_Tg_1


title: Adipose Tissue, HIV+preDM, 2118


title: 24_G0_Tg_4


title: sample5_day5_differentiation_medium

data_processing:
demultiplexed data were aligned and quantified using cellranger v7.1.0 using GRCh38 reference genome v2020
Assembly: GRCh38
Supplementary files format and content: HDF5 Feature-Barcode Matrix Format. Binary format of multidimensional arrays containing count of reads containing valid barcodes and UMIs as well as metadata on the libraries and gene sets/annotations.

source_name: Monocytes/macrophages

growth_protocol:
Cultivation on cell culture 24 well plates in IMDM containing 20% FCS, 1% Penicillin/Streptomycin, 2 mM L-Glutamine with:
complete medium: 10 ng/ml IL-3, 20 ng/ml IL-6, 20 ng/ml SCF, 20 ng/ml TPO, 20 ng/ml FLT3-L, 20 ng/ml GM-CSF
differentiation medium: 20 ng/ml GM-CSF, 20 ng/ml IFNγ, 100 ng/ml LPS

extract_protocol:
Cells were harvested via centrifugation and dilution to 1x106 cells/ml in PBS with 1% BSA. All samples had a viability of >95%. Cells were prepared according to the Handbook "Cell Preparation for Single Cell Protocols" by 10x Genomics.
10x Genomics Single Cell 3' v3

value: Monocytes/macrophages

value: Retrovirally transduced


title: 23_G0_Tg_3


title: Adipose Tissue, HIV+preDM, 2117


title: sample7_day12_differentiation_medium

value: Differentiation


title: sample6_day9_differentiation_medium


title: sample4_day2_differentiation_medium


title: sample3_day2_shield1_complete_medium


title: sample2_day0_shield1_complete_medium

value: Cultivation


title: CMD090

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

description: XimenaTorres_Llanos_AllSamples_Normalized_counts

data_processing:
BaseCall performed with CASAVA v1.8.2
Reads were aligned to the hg38 version of the human genome as reference using vSTAR 2.7.3 after removal of contaminants  (rDNA, tRNA, mtrDNA) were removed using Bowtie2 (version 2.2.5)
Reads aligned to STAR were quantified to the RefSeq Transcrips 96 and normalized by TMM and by log2 (x+1) transformation
Normalized counts were used to determine differential gene expression between responders and non-responders patients at day 15, at the end of the induction chemotherapy and in the true response groups  with Deseq2 library o Rstudio
All analyses were corrected for multiple comparisons at false discovery rate (FDR) 0.05 (at least)
Assembly: RefSeq Transcrips 96
Supplementary files format and content: txt files contain TMM normalized counts

extract_protocol:
RNA from MACS-sorted blasts were extracted using the Allprep mini kit and the robotic workstation QIAcube (Qiagen, Hilden, Germany) following the manufacturer's protocol
Paired-end libraries (2 x 75) were prepared (300ng per sample) using the TruSeq Stranded mRNA Library Prep kit

tag: patient classification

value: Responder

value: Diagnostic Fresh Bone Marrow


title: 28_G1_Tg_3

value: Control


title: Adipose Tissue, HIV+NonDM, 2115

value: HIV+ non-diabetic


title: 22_G0_Tg_2


title: 20_No_Tg_5


title: Adipose Tissue, HIV+preDM, 2114

value: Male

value: HIV+ prediabetic


title: Adipose Tissue, HIV+preDM, 2116


title: Adipose Tissue, HIV+preDM, 2113


title: sample1_day0_shield1_complete_medium


title: DFP084MX1

value: Refractory


title: 19_No_Tg_4

value: Kidney Glomeruli


title: Adipose Tissue, HIV+preDM, 2112

value: subcutaneous adipose tissue


title: AEM087DX


title: 21_G0_Tg_1


title: ESR082


title: KJM086


title: Adipose Tissue, HIV+preDM, 2111


title: 18_No_Tg_3


title: MGG080


title: NSH064


title: NB075


title: Adipose Tissue, HIV+DM, 2120

value: Female

value: HIV+ diabetic


title: 16_No_Tg_1


title: DC061DX


title: Adipose Tissue, HIV+preDM, 2110


title: 17_No_Tg_2


title: CZA072MX1


title: 15_G2_WT_3


title: sample8_day14_differentiation_medium


title: AFV057MX1


title: NAC081DX


title: JMC053


title: DIF054


title: Adipose Tissue, HIV+DM, 2109


title: Adipose Tissue, HIV+preDM, 2107


title: AFC050DXMX2


title: 13_G2_WT_1


title: JM040


title: JLG033


title: Adipose Tissue, HIV+preDM, 2103


title: Adipose Tissue, HIV+preDM, 2102


title: JEE037


title: 12_G1_WT_4


title: HCMMX1


title: 11_G1_WT_3


title: JSM026


title: Adipose Tissue, HIV+preDM, 2101


title: LSA023


title: 10_G1_WT_2


title: LLC022


title: Adipose Tissue, HIV+NonDM, 1182


title: DSR017


title: Adipose Tissue, HIV+preDM, 2108


title: JSR021


title: 9_G1_WT_1


title: 14_G2_WT_2


title: Adipose Tissue, HIV+NonDM, 1181


title: 8_G0_WT_3


title: KDA013


title: Adipose Tissue, HIV+preDM, 1180


title: 7_G0_WT_2


title: CAMs, 18 months, rep3

city: Caen

first: Damien

last: Levard

address: Bd Henri Becquerel

country: France

institute: Inserm U1237 PhIND

data_processing:
Image analysis and base calling were done by the Real Time Analysis Software (RTA) v3.7.17.
The resulting .cbcl files were converted into .fastq.gz files with the bcl2fastq v2.20 software.
Quality of raw data was evaluated with FastQC.
Poor quality sequences were trimmed or removed with fastp tool, with default parameters, to retain only good quality paired reads.
Illumina DRAGEN bio-IT Plateform (v3.8.4) was used for mapping on mm10 reference genome and quantification with gencode vM25 annotation gtf file.
Library orientation, library composition and coverage along transcripts were checked with Picard tools.
The GSEA analysis was started on the Gene sets derived from the GO Biological Process ontology (BP) database using the ClusterProfiler package, gseGO function. Then the Simplify function was used via GOSemSim to eliminate the redundant GO terms
Assembly: mm10
Supplementary files format and content: Format TSV: gene counts in each sample

extract_protocol:
Total RNA was extracted from FACS sorted mouse brain macrophages stabilized in RNAprotect buffer according to the “Purification of total RNA from animal and human cells” protocol of the RNeasy Plus Micro Kit (QIAGEN, Hilden, Germany).
The SMARTer Ultra Low Input RNA Kit for Sequencing v4 (Clontech Laboratories, Inc., Mountain View, CA, USA) was used to generate first strand cDNA from approximately 500 pg total-RNA. Double stranded cDNA was amplified by LD PCR (13 cycles) and purified via magnetic bead clean-up. Library preparation was carried out as described in the Illumina Nextera XT Sample Preparation Guide (Illumina, Inc., San Diego, CA, USA).
Equimolar amounts of each library were sequenced on an Illumina NextSeq 2000 instrument controlled by the NextSeq 2000 Control Software (NCS) v1.2.0.36376, using two 100 cycles P2 Flow Cell with the dual index, single-read (SR) run parameters

treatment_protocol: We FACS sorted (FACSAria, BD Biosciences) CD3-CD11b+CD45+CD206+ CAMs from brains of C57BL/6 mice (Janvier Labs) aged 2 months (young) and 18 months (old)

tag: strain

value: male

value: Brain

value: CAMs

value: 18 months


title: CAMs, 18 months, rep2


title: CAMs, 2 months, rep3

value: 2 months


title: CAMs, 18 months, rep1


title: Adipose Tissue, HIV+NonDM, 1179


title: 6_G0_WT_1


title: Adipose Tissue, HIV+NonDM, 1178


title: CAMs, 2 months, rep2


title: CAMs, 2 months, rep1


title: Meso3 T48

first: Caitlin

last: Tilsed

address: 407F 4312 Chestnut St

institute: The University of Pennsylvania

description:
timecourse.xls
Meso 3 48 h

data_processing:
The counts therefore are stoichiometrically equal to the number of transcripts in the sample and normalization by transcript length is not required. The HTG EdgeSeq data is transformed into gene counts per million counts (CPM) and normalized CPM gene reads were provided by HTG. Genes with low expression levels (less than 1 CPM were filtered leaving approximately 11,000 genes for analysis).
Supplementary files format and content: The date is in the form of two excel spreadsheets with CPM counts as provided by HTG
Library strategy: HTG Transcriptome Panel (HTP)

growth_protocol: PCTS of 300μm in thickness were prepared using a Compresstome (Precisionary Instruments LLC, VF-300). Tumor samples were mounted to the tissue plunger and embedded in 2% agarose, as previously described (4). Several PCTS were placed immediately in 10% formalin for fixation and labeled “0hr”. The remaining PCTS were placed on top of cell culture inserts (Millipore) in 24-well tissue culture plate and cultured in DMEM/F12 media supplemented with 10% FBS and 1% P/S at 37oC in a 5% CO2 incubator. At various time points (24 hrs, 48 hrs, and 72 hrs), supernatants were collected, and the PCTS were fixed in 10% formalin. All fixed PCTS were subsequently embedded in paraffin and standard 3 μm sections were cut and placed on glass slides. Slides were used for H&E or genomic analyses.

extract_protocol: Depending on the size, one to three marked slides from each PCTS were sent to HTG Molecular Diagnostics at the HTG VERI/O commercial laboratory in Tucson, AZ. For this study, we used a newly available HTG Transcriptome panel that interrogated 19,398 genes simultaneously (https://www.htgmolecular.com/assays/htp). HTG EdgeSeq probes target a single location of each RNA transcript resulting in a single probe sequence per RNA transcript. The counts therefore are stoichiometrically equal to the number of transcripts in the sample and normalization by transcript length is not required. The HTG EdgeSeq data is transformed into gene counts per million counts (CPM) and normalized CPM gene reads were provided by HTG. Genes with low expression levels (less than 1 CPM were filtered leaving approximately 11,000 genes for analysis).

tag: cancer type

value: mesothelioma

tag: timepoint


title: Meso3 T24

description:
timecourse.xls
Meso 3 24 h


title: Meso3 T0

description:
timecourse.xls
Meso 3 T0


title: Adipose Tissue, HIV+preDM, 1176

data_processing:
Samples were sequences in two batches on the Illumina NovaSeq 6000 platform using paired-end sequencing (2 x 150 pb)
Read quality was assessed and adapter read-through sequences were removed using fastp
Reads were mapped to the Human GENCODE release 34 hg38 using STAR v2.7.3a
FeatureCounts was used to assign reads to features using GENCODE v34 annotation
Assembly: GENCODE release 34 GRCh38
Supplementary files format and content: text file with raw counts from featureCounts

extract_protocol:
Total RNA was extracted from subcutaneous adipose tissue using Qiagen RNeasy Lipid Tissue Kit after mechanical lysis.
cDNA libraries were prepared with NEBNext Ultra II Directional RNA Library Prep Kits

tag: Sex


title: 4_No_WT_4

value: WT


title: Adipose Tissue, HIV+preDM, 1175


title: Meso2 T48

description:
timecourse.xls
Meso 2 48 h


title: Meso2 T72

description:
timecourse.xls
Meso 2 72 h


title: Meso2 T0

description:
timecourse.xls
Meso 2 T0


title: 2_No_WT_2


title: Meso2 T24

description:
timecourse.xls
Meso 2 24h


title: 3_No_WT_3


title: Adipose Tissue, HIV+NonDM, 1174


title: Meso1 T24

description:
timecourse.xls
Meso 1 24 h


title: Meso1 T48

description:
timecourse.xls
Meso 1 48 h


title: Adipose Tissue, HIV+preDM, 1173


title: Adipose Tissue, HIV+preDM, 1172


title: HNC43 T72

description:
timecourse.xls
HNC 43 72 h

value: head and neck


title: 1_No_WT_1

value: Control


title: Iris,Dorsal,4dpl,Rep3 [D4_Dorsal_3]

data_processing:
The first 10 base pairs of sequence read2 were hard trimmed to remove low-complexity bridge sequences introduced during library preparation. The reads were then quality and adapter trimmed with Trim Galore using parameters -q 5 --length 36 --stringency 1 -e 0.1.
Final transcript abundance was estimated with the Salmon alignment tool using the parameters -l ISR --numGibbsSamples 20 --seqBias --gcBias --reduceGCMemory -d.
Assembly: NVir_transcriptome.fasta
Supplementary files format and content: avgTPM.csv contains average TPM values of inferential replicates for each sample
Supplementary files format and content: NVir_transcriptome.fasta contains transcriptome used for quantification

organism: Notophthalmus viridescens

extract_protocol:
Dorsal iris tissues were collected from adult, wild-caught Notophthalmus viridescens. Three biological replicates were used per time point, with each biological replicate containing bilateral dorsal irises from 3 or 4 animals pooled together. The iris tissues were placed in 500μL of cold TRI Reagent (Zymo, R2050-1-50), vortexed, and stored at -80 °C until RNA extraction. RNA isolation was performed via extraction with 0.2 volumes chloroform followed by processing of the aqueous phase with the Direct-zol RNA Microprep Kit (Zymo, R2060) according to manufacturer’s instructions, including an in- column DNase I treatment.
Reverse transcription and library preparation were carried out with the Zymo-Seq RiboFree total RNA library Kit (Zymo, R3000) using 108 ng input RNA per reaction. RiboFree depletion was applied for 4 hours to deplete overrepresented transcripts, and final libraries were amplified with dual indexes (Zymo, D3096) for 13 PCR cycles.

value: dorsal iris tissue

tag: treatment/time point


title: HNC43 T48

description:
timecourse.xls
HNC 43 48 h


title: Meso1 T0

description:
timecourse.xls
Meso1 T0 ave


title: HNC43 T24

description:
timecourse.xls
HNC 43 24 h


title: 5_No_WT_5


title: Adipose Tissue, HIV+preDM, 1171

value: Male


title: Iris,Dorsal,4dpl,Rep2 [D4_Dorsal_2]


title: Iris,Dorsal,4dpl,Rep1 [D4_Dorsal_1]


title: Adipose Tissue, HIV+preDM, 1170

value: HIV+ prediabetic


title: HNC43 T0

description:
timecourse.xls
HNC43 T0


title: Adipose Tissue, HIV+preDM, 1169


title: Meso1 24hr

description:
fresh_24hr.xls
Meso 1 24


title: tp53 R242H/R242H 0 Gy, biol rep 2

city: Ottawa

first: Kim

last: Kobar

state: Ontario

address: 401 Smyth Rd

institute: Children's Hospital of Eastern Ontario Research Institute

data_processing:
The RNA-Seq data were mapped with STAR (v2.7) to generate BAM files and transcripts were quantified with RSEM using the zebrafish V4.3.2 transcript annotation.
Assembly: GRCz11
Supplementary files format and content: tab-delinated text file includes count matrix with each sample

organism: Danio rerio

source_name: whole embryo

growth_protocol: Larvae were maintained at 28C and samples were collected at 30 hpf.

extract_protocol:
Each RNA sample was extracted from 50 zebrafish embryos anesthetized with tricaine (MS-222) and homogenized in 500μL TRIzol reagent (Life Technologies, 15596026) using a 1mL syringe and 23G needle. Lysed samples were purified and DNAse treated using the Direct-zol RNA MicroPrep kit (Zymo Research Corperation, R2060). 4ug of total RNA from each sample were sent for RNA sequencing.
RNA Libraries were constructed for standard paired-read RNA sequencing by GeneWiz.

treatment_protocol: Larvae were exposed to either 0 or 30 Gy of irradiation at 24 hpf.

value: whole embryo

tag: Stage

value: 30 hpf

value: AB

value: 0 Gy


title: Adipose Tissue, HIV+NonDM, 1168

value: subcutaneous adipose tissue

tag: disease state

value: HIV+ non-diabetic


title: Iris,Dorsal,1dpl,Rep3 [D1_Dorsal_3]


title: Iris,Dorsal,1dpl,Rep2 [D1_Dorsal_2]


title: tp53 R242H/R242H 0 Gy, biol rep 1


title: Iris,Dorsal,1dpl,Rep1 [D1_Dorsal_1]


title: Adipose Tissue, HIV+NonDM, 1167

value: Female


title: Adipose Tissue, HIV+NonDM, 1166


title: tp53 R242H/R242H 30 Gy, biol rep 3

value: 30 Gy


title: Meso3 24hr

description:
fresh_24hr.xls
Meso 3 24 hrs


title: Meso3 fresh

description:
fresh_24hr.xls
Meso 3 fresh


title: tp53 R242H/R242H 30 Gy, biol rep 2


title: Iris,Dorsal,6hpl,Rep3 [D0.25_Dorsal_3]


title: Adipose Tissue, HIV+preDM, 1165


title: Meso2 24hr

description:
fresh_24hr.xls
Meso 2  24 hr


title: tp53 R242H/R242H 0 Gy, biol rep 3


title: tp53 R217H/R217H 0 Gy, biol rep 3


title: Meso2 fresh

description:
fresh_24hr.xls
Meso 2- fresh


title: Adipose Tissue, HIV+preDM, 1164


title: Iris,Dorsal,6hpl,Rep1 [D0.25_Dorsal_1]


title: tp53 R217H/R217H 0 Gy, biol rep 2


title: HNC43 24hr

description:
fresh_24hr.xls
HNC 43 24 hrs


title: Adipose Tissue, HIV+preDM, 1163


title: Iris,Dorsal,Intact,Rep3 [D0_Dorsal_3]

value: Intact


title: tp53 R217H/R217H 0 Gy, biol rep 1


title: Adipose Tissue, HIV+preDM, 1162


title: HNC43 fresh

description:
fresh_24hr.xls
hnc43


title: Iris,Dorsal,Intact,Rep2 [D0_Dorsal_2]


title: Meso1 fresh

description:
fresh_24hr.xls
Meso 1- fresh


title: tp53 R217H/R217H 30 Gy, biol rep 2


title: Adipose Tissue, HIV+NonDM, 1161


title: HNC27 24hr

description:
fresh_24hr.xls
HNC27_24 hrs


title: tp53 R217H/R217H 30 Gy, biol rep 3


title: Iris,Dorsal,Intact,Rep1 [D0_Dorsal_1]


title: tp53 R242H/R242H 30 Gy, biol rep 1


title: Iris,Dorsal,6hpl,Rep2 [D0.25_Dorsal_2]


title: Sugar glider (Sample1798)

first: Olga

last: Dudchenko

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Short-read assembly using w2rap (Clavijo, 2017); Hi-C-guided genome assembly (Juicer, 3D-DNA, JBAT); RagTag assembler (Alonge et al., 2022) for Dactylopsila trivirgata and Distoechurus pennatus
Assembly: Generated as part of the study
Supplementary files format and content: fasta.gz: chromosome-length nucleotide sequences generated usign Hi-C-guided genome assembly; RagTag assisted assemblies for Dactylopsila trivirgata and Distoechurus pennatus
Library strategy: In situ Hi-C; ClaSeek PCR-free DNA-Seq.

organism: Petaurus breviceps

source_name: kidney

extract_protocol:
Extractions for WGS libraries were done using DNeasy blood & tissue kit
The Hi-C libraries were prepared following the in situ Hi-C strategy (Rao, Huntley et al., 2014). Briefly, cells or tissue were crosslinked and then lysed with nuclei permeabilized but still intact. DNA was then restricted and the overhangs filled in incorporating a biotinylated base. Free ends were then ligated together in situ. Crosslinks were reversed, the DNA was sheared to 300-500bp and then biotinylated ligation junctions were recovered with streptavidin beads. Afterward DNA was handled according to standard Illumina library construction protocol. DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo-) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3 end. After adapter ligation DNA was PCR amplified with Illumina primers and library fragments of 400-600 bp (insert plus adaptor and PCR primer sequences) were purified using SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on various Illumina instruments following the manufacturer's protocols. Fpr the tammar wallaby, a short insert-size PCR-free DNA-Seq library was prepared following the ClaSeek protocol.

value: kidney


title: HNC21 24hr

description:
fresh_24hr.xls
HNC21  24Tumor  n=2


title: HNC27 fresh

description:
fresh_24hr.xls
HNC27_fresh


title: Coppery ringtail possum (Sample1791)

organism: Pseudochirops cupreus


title: tp53 R217H/R217H 30 Gy, biol rep 1


title: Adipose Tissue, HIV+NonDM, 1159


title: Adipose Tissue, HIV+preDM, 1158


title: HNC21 fresh

description:
fresh_24hr.xls
HNC21 HNC_fresh


title: Common wombat (Sample0158)

organism: Vombatus ursinus

source_name: blood

value: blood


title: Adipose Tissue, HIV+preDM, 1157


title: tp53 null/null 0 Gy, biol rep 3

value: tp53 null/null


title: tp53 null/null 0 Gy, biol rep 2


title: tp53 null/null 0 Gy, biol rep 1


title: CRISPRCas9_TeloHAEC_CALCRL_del_rep3

city: Kuopio

first: Minna

middle: U

last: Kaikkonen

address: Neulaniementie 2

country: Finland

institute: A.I.Virtanen Institute for Molecular Sciences

data_processing:
Base-calling was perform during the sequencing run by RTA version 2.11.3 running under NextSeq Control Software version 4.0.2.7.  The sequencing reads were processed using the nf-core RNA-seq pipeline (version 3.1; (Ewels et al. 2020)) with the hg19 genome. Genes with low expression were filtered out with the filterByExpr function of the edgeR package (version 3.24.3; (Robinson et al. 2010)) using minimum count 5 and minimum total count 15.
Assembly: hg19
Supplementary files format and content: siCALCRL: Nf-core RNA-seq pipeline was used to process fastq files and derive gene counts
Supplementary files format and content: CRISPR-Cas9-del: Nf-core RNA-seq pipeline was used to process fastq files and derive gene counts

source_name: TeloHAEC

growth_protocol: Immortalized human aortic endothelial cells (teloHAECs) were purchased from ATCC and cultured in Vascular Cell Basal Medium (ATCC PCS-100-030), supplemented with Vascular Endothelial Cell Growth Kit-VEGF (ATCC PCS-100-041), 100 U/ml penicillin and 100 µg/ml streptomycin. Cells were incubated at 37°C in 5% CO2 and passaged every 3 days.

extract_protocol:
For siRNA treatment, the RNA was extracted using RNeasyPlus Micro kit (QIAGEN). RNA-Seq library preparation was carried out using QuantSeq 3' mRNA-seq Library Prep Kit FWD for Illumina (Lexogen, Vienna, Austria) according to the manufacturer’s instructions. The resultant library was quantified using Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and its quality was checked with Bioanalyzer using High Sensitivity DNA Kit (Agilent Technologies). Individual libraries were pooled in equimolar ratio (4 nM total) and sequenced with the NextSeq 550 platform (Illumina, San Diego, California) with a single end high output kit using read length 86 cycles.
CRISPR-Cas9: To analyze the efficiency of enhancer deletion, genomic DNA was extracted using NucleoSpin tissue kit (Macherey-Nagel, Düren, Germany) and amplified by PCR using specific primers flanking the deletion sites using DreamTaq DNA Polymerase (EP0701, Thermo Fisher Scientific). PCR products were then analyzed by electrophoresis in 1% agarose gel. To analyze the effects of enhancer deletion on cis target gene expression, the RNA was extracted using RNeasyPlus Micro kit (QIAGEN).  RNA-Seq library preparation was carried out using QuantSeq 3' mRNA-seq Library Prep Kit FWD for Illumina (Lexogen, Vienna, Austria) according to the manufacturer’s instructions. The resultant library was quantified using Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and its quality was checked with Bioanalyzer using High Sensitivity DNA Kit (Agilent Technologies). Individual libraries were pooled in equimolar ratio (4 nM total) and sequenced with the NextSeq 550 platform (Illumina, San Diego, California) with a single end high output kit using read length 86 cycles.

treatment_protocol:
For siRNA treatment, TeloHAEC were reverse transfected with Lipofectamine RNAiMAX transfection reagent (Thermo Fisher) according to the manufacturer’s instructions. The target-specific Silencer Select siRNAs for CALCRL and scrambled siRNA were obtained from Thermo Fisher (s19889 and s19890). Cells were lysed 24 h after transfection for RNA extraction.
For CRISPR-Cas9-mediated deletion of target region was performed using the Alt-R CRISPR-Cas9 System (Integrated DNA technologies; IDT, Coralville, Iowa). Briefly, CRISPR-Cas9 single gRNAs flanking the target enhancers were designed using an online CRISPR design tool (https://eu.idtdna.com/site/order/designtool/index/CRISPR_SEQUENCE) and ordered from IDT as crRNAs. For control, the positive control (crRNA targeting HPRT) from the Alt-R CRISPR-Cas9 Human Control Kit (IDT) were used. These crRNAs were annealed to a tracrRNA (IDT) and complexed with Cas9 endonuclease (S.p. HiFi Cas9 Nuclease V3; IDT) to form the ribonucleoprotein complex (RNP). The RNP complexes were then delivered into teloHAEC cells per replicate by electroporation using the Neon transfection system (Invitrogen) with a 1350 V pulse of 30 ms width, following IDT CRISPR genome editing protocol for RNP electroporation with Neon Transfection system. Two days later, transfected cells were collected for RNA and gDNA extraction.


title: Hi-C of Elephas maximus DNA Zoo Sample3070

city: Houston

description:
ASM1433276v1.hic
ASM1433276v1_HiC.fasta.gz
ASM1433276v1.rawchrom.hic
EM_skin_CRUSH_Loxafr3.0_HiC.bedgraph
EM_skin_Loxafr3.0_HiC.hic
EM_skin_Loxafr3.0_HiC_30.hic
EM_skin_sub_Loxafr3.0_HiC.hic
EM_skin_sub_Loxafr3.0_HiC_30.hic
EM_skin_MamPri_Loxafr3.0_assisted_HiC.hic
EM_skin_MamPri_Loxafr3.0_assisted_HiC_30.hic
EM_skin_MamPri_ASM1433276v1_assisted_HiC.hic
EM_skin_MamPri_ASM1433276v1_assisted_HiC_30.hic

data_processing:
Hi-C-guided genome assembly (3D-DNA, JBAT)
Reference-guided 3D genome assembly (Anonamos, 3D-DNA, JBAT)
Construction of the chromosome-length Hi-C contact map (BWA, Juicer, 3D-DNA)
liftover (KentUtils, 3D-DNA)
Gene annotation (TOGA)
Compartment annotation (CRUSH)
Loop calling and aggregate analysis (HiCCUPS, Juicer Tools, SIP, SIP META)
Aggregate chromosome analysis (3D-DNA)
Modeling of 3D structures of woolly mammoth chromosomes (OpenMiChroM)
DNA degradation simulations (NuChroM, custom script)
Assembly: The following existing genome builds were used in parts of the study: Loxafr3.0 (GCA_000001905.1), ASM1433276v1 (GCA_014332765.1), EquCab2.0 (GCF_000002305.2), ASM303372v1 (GCA_003033725.1), bosTau9 (GCF_002263795.3), ASM651725v1 (GCF_006517255.1), ASM3043605v1 (GCF_030436055.1), ASM331443v2 (GCF_003314435.2), hg38, hg19.
Supplementary files format and content: fasta.gz: chromosome-length nucleotide sequences generated usign Hi-C-guided genome assembly
Supplementary files format and content: hic: contact maps generated by aligning Hi-C data to reference sequences. In addition to "standard" hic maps build against chromosome-length references included are "assembly" maps generated by 3D-DNA for before and after genome assembly and an aggregate chromosome analysis (ACA) map.
Supplementary files format and content: bedpe: chromatin loops
Supplementary files format and content: bedgraph: A/B compartment annotations
Supplementary files format and content: sw: HDF5-based file for storing 3D structure ensembles
Supplementary files format and content: assembly: text file describing the relationship between the draft assembly and the chromosome-length upgrade
Supplementary files format and content: bed: gene annotations

organism: Elephas maximus indicus

source_name: skin

extract_protocol:
The protocol is described in detail in Sandoval-Velasco, Dudchenko, Rodríguez, Pérez Estrada et al., 2024. Briefly, PaleoHi-C is a a modified in situ Hi-C protocol, tailored towards working with highly degraded samples. The principal modifications were: (i) immediate preservation in the field using ethanol to reduce microbial activity; and (ii) sequestration of chromatin bodies on beads; (iii) removal of shearing and size selection given the lack of high molecular weight DNA; and (iv) library amplification using a paleo-compatible workflow
Library contruction protocol is described in detail in Sandoval-Velasco, Dudchenko, Rodríguez, Pérez Estrada et al., 2024.
Modified Hi-C.

value: skin


title: CRISPRCas9_TeloHAEC_CALCRL_del_rep2

value: Immortalized human aortic endothelial cells (teloHAECs)


title: Adipose Tissue, HIV+NonDM, 1150


title: Adipose Tissue, HIV+preDM, 1160


title: tp53 null/null 30 Gy, biol rep 3


title: Hi-C of Elephas maximus DNA Zoo Sample3085

description:
ASM1433276v1.hic
ASM1433276v1_HiC.fasta.gz
ASM1433276v1.rawchrom.hic
EM_ovary_Loxafr3.0_HiC.hic
EM_ovary_Loxafr3.0_HiC_30.hic
EM_ovary_MamPri_Loxafr3.0_assisted_HiC.hic
EM_ovary_MamPri_Loxafr3.0_assisted_HiC_30.hic
EM_ovary_MamPri_ASM1433276v1_assisted_HiC.hic
EM_ovary_MamPri_ASM1433276v1_assisted_HiC_30.hic

source_name: ovary

value: ovary


title: Hi-C of Elephas maximus DNA Zoo Sample3076

description:
ASM1433276v1.hic
ASM1433276v1_HiC.fasta.gz
ASM1433276v1.rawchrom.hic
EM_liver_Loxafr3.0_HiC.hic
EM_liver_Loxafr3.0_HiC_30.hic
EM_liver_MamPri_Loxafr3.0_assisted_HiC.hic
EM_liver_MamPri_Loxafr3.0_assisted_HiC_30.hic
EM_liver_MamPri_ASM1433276v1_assisted_HiC.hic
EM_liver_MamPri_ASM1433276v1_assisted_HiC_30.hic

source_name: liver

value: liver


title: tp53 null/null 30 Gy, biol rep 2


title: CRISPRCas9_TeloHAEC_CALCRL_del_rep1


title: Adipose Tissue, HIV+NonDM, 1133

source_name: subcutaneous adipose tissue

value: Male


title: tp53 null/null 30 Gy, biol rep 1

value: whole embryo


title: CRISPRCas9_TeloHAEC_CALCRL_ctrl_rep2

value: CRISPR control


title: Hi-C of Elephas maximus DNA Zoo Sample3074

description:
ASM1433276v1.hic
ASM1433276v1_HiC.fasta.gz
ASM1433276v1.rawchrom.hic
EM_brain_Loxafr3.0_HiC.hic
EM_brain_Loxafr3.0_HiC_30.hic
EM_brain_MamPri_Loxafr3.0_assisted_HiC.hic
EM_brain_MamPri_Loxafr3.0_assisted_HiC_30.hic
EM_brain_MamPri_ASM1433276v1_assisted_HiC.hic
EM_brain_MamPri_ASM1433276v1_assisted_HiC_30.hic

source_name: brain

value: brain


title: casper 0 Gy, biol rep 3

value: 30 hpf

value: AB

value: casper

value: 0 Gy


title: CRISPRCas9_TeloHAEC_CALCRL_ctrl_rep1


title: casper 0 Gy, biol rep 2


title: TeloHAEC_CALCRL_scrambled_siRNA_rep4

value: si-scrambled


title: Hi-C of Bos taurus DNA Zoo Sample6779, Freeze-dried beef heart, Natural Rapport brand

description:
HIC16986.hic
HIC16986_30.hic

organism: Bos taurus

source_name: heart

value: heart

value: Freeze-dried beef heart


title: Hi-C of Bos taurus DNA Zoo Sample6780, Freeze-dried beef heart, smallBatch brand

description:
HIC16987.hic
HIC16987_30.hic


title: Hi-C of Elephas maximus indicus DNA Zoo Sample3070

description:
EM_derm_CRUSH_Loxafr3.0_HiC.bedgraph
EM_skin_derm_Loxafr3.0_HiC.hic
EM_skin_derm_Loxafr3.0_HiC_30.hic


title: Adipose Tissue, HIV+preDM, 1129

value: subcutaneous adipose tissue

value: HIV+ prediabetic


title: Adipose Tissue, HIV+preDM, 1152


title: casper 0 Gy, biol rep 1


title: TeloHAEC_CALCRL_scrambled_siRNA_rep3


title: casper 30 Gy, biol rep 3

value: 30 Gy


title: Hi-C of Bos taurus DNA Zoo Sample6244, Buc-ee's teriyaki beef jerky, rep2

description:
HIC16743+HIC16744.hic
HIC16743+HIC16744_30.hic

source_name: missing

value: missing

value: Beef jearky


title: Hi-C of Bos taurus DNA Zoo Sample6244, Buc-ee's teriyaki beef jerky, rep1


title: Adipose Tissue, HIV+preDM, 1137

value: Female


title: CRISPRCas9_TeloHAEC_CALCRL_ctrl_rep3

value: Immortalized human aortic endothelial cells (teloHAECs)


title: TeloHAEC_CALCRL_scrambled_siRNA_rep1


title: TeloHAEC_CALCRL_scrambled_siRNA_rep2


title: casper 30 Gy, biol rep 1

value: whole embryo


title: Adipose Tissue, HIV+NonDM, 1125

value: Male

value: HIV+ non-diabetic


title: LVC063

value: Responder

value: Diagnostic Fresh Bone Marrow


title: Adipose Tissue, HIV+NonDM, 1130


title: Hi-C of Bos taurus DNA Zoo Sample6767, Fresh beef sirloin ~24hpm, rep1

description:
HIC16954+HIC16956.hic
HIC16954+HIC16956_30.hic

source_name: sirloin

value: sirloin

value: Fresh beef sirloin ~24hpm, rep1


title: Hi-C of Bos taurus DNA Zoo Sample6767, Fresh beef sirloin ~24hpm, rep2

value: Fresh beef sirloin ~24hpm, rep2


title: Adipose Tissue, HIV+NonDM, 1127


title: Adipose Tissue, HIV+NonDM, 1131


title: TeloHAEC_CALCRL_siRNA_kockout_rep3

value: si-CALCRL


title: Adipose Tissue, HIV+NonDM, 1123


title: Hi-C of Bos taurus DNA Zoo Sample6774, Beef heart jerky, rep2

description:
HIC16963+HIC16964+HIC16982.hic
HIC16963+HIC16964+HIC16982_30.hic

value: heart

value: Beef heart jerky, rep2


title: Adipose Tissue, HIV+NonDM, 1120

value: subcutaneous adipose tissue


title: casper 30 Gy, biol rep 2

value: 30 hpf

value: AB

value: casper

value: 30 Gy


title: TeloHAEC_CALCRL_siRNA_kockout_rep2

value: Immortalized human aortic endothelial cells (teloHAECs)


title: Adipose Tissue, HIV+NonDM, 1119


title: TeloHAEC_CALCRL_siRNA_kockout_rep4


title: Hi-C of Bos taurus DNA Zoo Sample6774, Beef heart jerky, rep3

value: Beef heart jerky, rep3


title: Adipose Tissue, HIV+NonDM, 1122

value: Female


title: TeloHAEC_CALCRL_siRNA_kockout_rep1


title: Adipose Tissue, HIV+NonDM, 1128

value: HIV+ non-diabetic


title: Hi-C of Bos taurus DNA Zoo Sample6770, DIY sirloin jerky in toaster oven, dehydtrated for 6h

description:
HIC16976.hic
HIC16976_30.hic

value: DIY sirloin jerky in toaster oven, dehydrated for 6h


title: Hi-C of Bos taurus DNA Zoo Sample6774, Beef heart jerky, rep1

value: Beef heart jerky, rep1


title: Hi-C of Bos taurus DNA Zoo Sample6770, DIY sirloin jerky in toaster oven, dehydtrated for 3h

description:
HIC16975.hic
HIC16975_30.hic

value: sirloin

value: DIY sirloin jerky in toaster oven, dehydrated for 3h


title: Adipose Tissue, HIV+NonDM, 1118

value: Male


title: Hi-C of Bos taurus DNA Zoo Sample6770, DIY sirloin jerky in toaster oven, dehydrated for 2h

description:
HIC16974.hic
HIC16974_30.hic


title: Adipose Tissue, HIV+NonDM, 1117